diff --git a/fixtures/contracts/portfolio-command-center-v1/manifest.json b/fixtures/contracts/portfolio-command-center-v1/manifest.json
index 56d6b7e9..938b7c4a 100644
--- a/fixtures/contracts/portfolio-command-center-v1/manifest.json
+++ b/fixtures/contracts/portfolio-command-center-v1/manifest.json
@@ -24,7 +24,7 @@
   "portfolio_truth_schema_version": "0.11.0",
   "producer": {
     "artifact_path": "fixtures/contracts/portfolio-command-center-v1/portfolio-truth.json",
-    "artifact_sha256": "ba3000833f1cd9c89442948ebe51f7e405e7832333a69c6f7347fb2fbfae254a",
+    "artifact_sha256": "5b12c9851e43f82bcaf872f900539d5a5b67da9d405a7e73f7d3a20bfcdb9eae",
     "generator": "src.portfolio_truth_contract_fixture:build_contract_fixture",
     "manifest_path": "fixtures/contracts/portfolio-command-center-v1/manifest.json",
     "repository": "saagpatel/GithubRepoAuditor"
diff --git a/fixtures/contracts/portfolio-command-center-v1/portfolio-truth.json b/fixtures/contracts/portfolio-command-center-v1/portfolio-truth.json
index 6cd0e2e7..269829d7 100644
--- a/fixtures/contracts/portfolio-command-center-v1/portfolio-truth.json
+++ b/fixtures/contracts/portfolio-command-center-v1/portfolio-truth.json
@@ -64,7 +64,7 @@
   "derivation_policy_version": "portfolio_attention.v3",
   "exclusions": {
     "counts": {},
-    "policy_version": "workspace_discovery.v2"
+    "policy_version": "workspace_discovery.v3"
   },
   "generated_at": "2026-08-01T00:00:00+00:00",
   "inputs": {
@@ -1632,6 +1632,15 @@
     },
     "catalog_errors": [],
     "catalog_warnings": [],
+    "checkout_collisions": {
+      "ambiguous_group_count": 0,
+      "discarded_checkout_count": 0,
+      "full_clone_group_count": 0,
+      "group_count": 0,
+      "groups": [],
+      "schema_version": "CheckoutCollisionSummaryV1",
+      "state": "observed"
+    },
     "context_quality_counts": {
       "boilerplate": 1,
       "full": 1,
diff --git a/output/demo/portfolio-truth-history-01.json b/output/demo/portfolio-truth-history-01.json
index ed19d76e..7ac14a9d 100644
--- a/output/demo/portfolio-truth-history-01.json
+++ b/output/demo/portfolio-truth-history-01.json
@@ -1,17 +1,17 @@
 {
   "schema_version": "0.11.0",
-  "generated_at": "2026-06-08T22:09:43.833784+00:00",
+  "generated_at": "2026-06-09T20:46:39.243078+00:00",
   "derivation_policy_version": "portfolio_attention.v3",
   "producer": {},
   "inputs": {
     "catalog": {
       "source_id": "portfolio-catalog",
       "sha256": null,
-      "observed_at": "2026-06-08T22:09:43.833784+00:00"
+      "observed_at": "2026-06-09T20:46:39.243078+00:00"
     },
     "workspace": {
       "source_id": "projects-root",
-      "observed_at": "2026-06-08T22:09:43.833784+00:00"
+      "observed_at": "2026-06-09T20:46:39.243078+00:00"
     },
     "notion": {
       "mode": "unavailable",
@@ -21,7 +21,7 @@
     "github_security": {
       "source_id": "github-security-coverage-receipt",
       "schema_version": "GitHubSecurityCoverageReceiptV1",
-      "produced_at": "2026-06-08T22:09:43.833784+00:00",
+      "produced_at": "2026-06-09T20:46:39.243078+00:00",
       "state": "fresh",
       "age_hours": 0.0,
       "producer_commit": "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
@@ -89,13 +89,22 @@
     }
   ],
   "exclusions": {
-    "policy_version": "workspace_discovery.v2",
+    "policy_version": "workspace_discovery.v3",
     "counts": {}
   },
   "workspace_root": "/demo-workspace",
   "source_summary": {
     "workspace_root": "/demo-workspace",
     "project_count": 40,
+    "checkout_collisions": {
+      "schema_version": "CheckoutCollisionSummaryV1",
+      "state": "observed",
+      "group_count": 0,
+      "full_clone_group_count": 0,
+      "ambiguous_group_count": 0,
+      "discarded_checkout_count": 0,
+      "groups": []
+    },
     "catalog_errors": [],
     "catalog_warnings": [],
     "legacy_registry_rows": 40,
@@ -297,7 +306,7 @@
         "run_instructions_present": false,
         "known_risks_present": false,
         "next_recommended_move_present": false,
-        "last_meaningful_activity_at": "2025-11-30T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-01T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": true,
         "attention_state": "archived",
@@ -348,7 +357,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-06-08T22:09:43.833784+00:00",
+        "observed_at": "2026-06-09T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/archive/gossamer-ridge",
           "head": "8adcd37f116d59aaf20b40eaa0cdeab86dfb94991e5a55bc38d5dd9fe605999a",
@@ -486,7 +495,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2025-11-30T22:09:43.833784+00:00"
+          "detail": "2025-12-01T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -582,7 +591,7 @@
         "run_instructions_present": false,
         "known_risks_present": false,
         "next_recommended_move_present": false,
-        "last_meaningful_activity_at": "2025-11-30T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-01T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": true,
         "attention_state": "archived",
@@ -633,7 +642,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-06-08T22:09:43.833784+00:00",
+        "observed_at": "2026-06-09T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/archive/hollow-tessera",
           "head": "2bde0b8985233649f988ae61d8e1a350bd9b26afe38ba77b1574fc9c7c62ddde",
@@ -771,7 +780,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2025-11-30T22:09:43.833784+00:00"
+          "detail": "2025-12-01T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -867,7 +876,7 @@
         "run_instructions_present": false,
         "known_risks_present": false,
         "next_recommended_move_present": false,
-        "last_meaningful_activity_at": "2025-11-30T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-01T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": true,
         "attention_state": "archived",
@@ -918,7 +927,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-06-08T22:09:43.833784+00:00",
+        "observed_at": "2026-06-09T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/archive/indigo-palisade",
           "head": "f0dbcdef099e2f12e660a25ffb9724167b98e93d62a073c88ba225ab08c72b01",
@@ -1056,7 +1065,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2025-11-30T22:09:43.833784+00:00"
+          "detail": "2025-12-01T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -1152,7 +1161,7 @@
         "run_instructions_present": false,
         "known_risks_present": false,
         "next_recommended_move_present": false,
-        "last_meaningful_activity_at": "2025-11-30T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-01T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": true,
         "attention_state": "archived",
@@ -1203,7 +1212,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-06-08T22:09:43.833784+00:00",
+        "observed_at": "2026-06-09T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/archive/jetty-marquee",
           "head": "4e37a4b211dcf18c9df7cc6741b9553564f7833d2c15bae2391c3ad96ab523a7",
@@ -1341,7 +1350,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2025-11-30T22:09:43.833784+00:00"
+          "detail": "2025-12-01T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -1437,7 +1446,7 @@
         "run_instructions_present": false,
         "known_risks_present": false,
         "next_recommended_move_present": false,
-        "last_meaningful_activity_at": "2025-11-30T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-01T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": true,
         "attention_state": "archived",
@@ -1488,7 +1497,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-06-08T22:09:43.833784+00:00",
+        "observed_at": "2026-06-09T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/archive/kindling-arbor",
           "head": "f20d19345ed9ba389f768e1a1655904e97a05296ed26879867f8d512e8b60e55",
@@ -1626,7 +1635,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2025-11-30T22:09:43.833784+00:00"
+          "detail": "2025-12-01T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -1722,7 +1731,7 @@
         "run_instructions_present": false,
         "known_risks_present": false,
         "next_recommended_move_present": false,
-        "last_meaningful_activity_at": "2025-11-30T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-01T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": true,
         "attention_state": "archived",
@@ -1773,7 +1782,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-06-08T22:09:43.833784+00:00",
+        "observed_at": "2026-06-09T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/archive/lattice-bezel",
           "head": "2610bee9ecd0d6021c000352f707de6bd4b14266961546fde08835a4501e1f8f",
@@ -1911,7 +1920,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2025-11-30T22:09:43.833784+00:00"
+          "detail": "2025-12-01T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -2007,7 +2016,7 @@
         "run_instructions_present": false,
         "known_risks_present": false,
         "next_recommended_move_present": false,
-        "last_meaningful_activity_at": "2025-11-30T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-01T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": true,
         "attention_state": "archived",
@@ -2058,7 +2067,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-06-08T22:09:43.833784+00:00",
+        "observed_at": "2026-06-09T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/archive/mica-turnstile",
           "head": "db63c3180e5bc5c00c912da9d9cca2b89034693953974b9892be5b94062b1e82",
@@ -2196,7 +2205,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2025-11-30T22:09:43.833784+00:00"
+          "detail": "2025-12-01T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -2292,7 +2301,7 @@
         "run_instructions_present": false,
         "known_risks_present": false,
         "next_recommended_move_present": false,
-        "last_meaningful_activity_at": "2025-11-30T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-01T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": true,
         "attention_state": "archived",
@@ -2343,7 +2352,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-06-08T22:09:43.833784+00:00",
+        "observed_at": "2026-06-09T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/archive/nocturne-spar",
           "head": "6f5e62b92a004211d4adc5986895c2b75063d4eb7400b67dba09befb5d02ca69",
@@ -2481,7 +2490,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2025-11-30T22:09:43.833784+00:00"
+          "detail": "2025-12-01T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -2580,7 +2589,7 @@
         "run_instructions_present": true,
         "known_risks_present": true,
         "next_recommended_move_present": true,
-        "last_meaningful_activity_at": "2026-06-06T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2026-06-07T20:46:39.243078+00:00",
         "activity_status": "active",
         "archived": false,
         "attention_state": "decision-needed",
@@ -2611,7 +2620,7 @@
         "cohort_policy": "portfolio-default-attention-v1",
         "receipt_schema_version": "GitHubSecurityCoverageReceiptV1",
         "receipt_state": "fresh",
-        "source_produced_at": "2026-06-08T22:09:43.833784+00:00",
+        "source_produced_at": "2026-06-09T20:46:39.243078+00:00",
         "providers": {
           "dependabot": {
             "state": "observed",
@@ -2626,7 +2635,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-06-08T22:09:43.833784+00:00",
+            "observed_at": "2026-06-09T20:46:39.243078+00:00",
             "pagination_complete": true,
             "counts": {
               "critical": 1,
@@ -2649,7 +2658,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-06-08T22:09:43.833784+00:00",
+            "observed_at": "2026-06-09T20:46:39.243078+00:00",
             "pagination_complete": true,
             "counts": {
               "critical": 0,
@@ -2672,7 +2681,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-06-08T22:09:43.833784+00:00",
+            "observed_at": "2026-06-09T20:46:39.243078+00:00",
             "pagination_complete": true,
             "counts": {
               "open": 0
@@ -2700,7 +2709,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-06-08T22:09:43.833784+00:00",
+        "observed_at": "2026-06-09T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/flagship/aurora-ledger",
           "head": "3fe2c06cdac61e60f0abced439f4c0ea2312d54dd314cf09631cc032f5f30549",
@@ -2719,7 +2728,7 @@
           "state": "observed",
           "reason_code": "observed",
           "reason": null,
-          "observed_at": "2026-06-08T22:09:43.833784+00:00",
+          "observed_at": "2026-06-09T20:46:39.243078+00:00",
           "default_branch": "main",
           "head_sha": "3fe2c06cdac61e60f0abced439f4c0ea2312d54dd314cf09631cc032f5f30549",
           "archived": false
@@ -2846,7 +2855,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2026-06-06T22:09:43.833784+00:00"
+          "detail": "2026-06-07T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -2944,7 +2953,7 @@
         "run_instructions_present": true,
         "known_risks_present": true,
         "next_recommended_move_present": true,
-        "last_meaningful_activity_at": "2026-06-06T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2026-06-07T20:46:39.243078+00:00",
         "activity_status": "active",
         "archived": false,
         "attention_state": "decision-needed",
@@ -2975,7 +2984,7 @@
         "cohort_policy": "portfolio-default-attention-v1",
         "receipt_schema_version": "GitHubSecurityCoverageReceiptV1",
         "receipt_state": "fresh",
-        "source_produced_at": "2026-06-08T22:09:43.833784+00:00",
+        "source_produced_at": "2026-06-09T20:46:39.243078+00:00",
         "providers": {
           "dependabot": {
             "state": "observed",
@@ -2990,7 +2999,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-06-08T22:09:43.833784+00:00",
+            "observed_at": "2026-06-09T20:46:39.243078+00:00",
             "pagination_complete": true,
             "counts": {
               "critical": 0,
@@ -3013,7 +3022,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-06-08T22:09:43.833784+00:00",
+            "observed_at": "2026-06-09T20:46:39.243078+00:00",
             "pagination_complete": true,
             "counts": {
               "critical": 0,
@@ -3036,7 +3045,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-06-08T22:09:43.833784+00:00",
+            "observed_at": "2026-06-09T20:46:39.243078+00:00",
             "pagination_complete": true,
             "counts": {
               "open": 0
@@ -3064,7 +3073,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-06-08T22:09:43.833784+00:00",
+        "observed_at": "2026-06-09T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/flagship/basalt-relay",
           "head": "5756778ed7c8d9b653dc146593c1e6d370d8db2c2e3d9d4a482928cef1535a75",
@@ -3083,7 +3092,7 @@
           "state": "observed",
           "reason_code": "observed",
           "reason": null,
-          "observed_at": "2026-06-08T22:09:43.833784+00:00",
+          "observed_at": "2026-06-09T20:46:39.243078+00:00",
           "default_branch": "main",
           "head_sha": "5756778ed7c8d9b653dc146593c1e6d370d8db2c2e3d9d4a482928cef1535a75",
           "archived": false
@@ -3210,7 +3219,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2026-06-06T22:09:43.833784+00:00"
+          "detail": "2026-06-07T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -3307,7 +3316,7 @@
         "run_instructions_present": true,
         "known_risks_present": true,
         "next_recommended_move_present": true,
-        "last_meaningful_activity_at": "2026-06-06T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2026-06-07T20:46:39.243078+00:00",
         "activity_status": "active",
         "archived": false,
         "attention_state": "decision-needed",
@@ -3338,7 +3347,7 @@
         "cohort_policy": "portfolio-default-attention-v1",
         "receipt_schema_version": "GitHubSecurityCoverageReceiptV1",
         "receipt_state": "fresh",
-        "source_produced_at": "2026-06-08T22:09:43.833784+00:00",
+        "source_produced_at": "2026-06-09T20:46:39.243078+00:00",
         "providers": {
           "dependabot": {
             "state": "observed",
@@ -3353,7 +3362,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-06-08T22:09:43.833784+00:00",
+            "observed_at": "2026-06-09T20:46:39.243078+00:00",
             "pagination_complete": true,
             "counts": {
               "critical": 2,
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@@ -12778,7 +12787,7 @@
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         "known_risks_present": true,
         "next_recommended_move_present": true,
-        "last_meaningful_activity_at": "2025-11-30T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-01T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": false,
         "attention_state": "parked",
@@ -12829,7 +12838,7 @@
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-        "observed_at": "2026-06-08T22:09:43.833784+00:00",
+        "observed_at": "2026-06-09T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/studio/yarrow-spindle",
           "head": "f618c22516c338789613aa8b2c965c88debc501e1932019921254bd1efc8b012",
@@ -12967,7 +12976,7 @@
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-          "detail": "2025-11-30T22:09:43.833784+00:00"
+          "detail": "2025-12-01T20:46:39.243078+00:00"
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diff --git a/output/demo/portfolio-truth-history-02.json b/output/demo/portfolio-truth-history-02.json
index 08e170cf..503c0ebc 100644
--- a/output/demo/portfolio-truth-history-02.json
+++ b/output/demo/portfolio-truth-history-02.json
@@ -1,17 +1,17 @@
 {
   "schema_version": "0.11.0",
-  "generated_at": "2026-06-15T22:09:43.833784+00:00",
+  "generated_at": "2026-06-16T20:46:39.243078+00:00",
   "derivation_policy_version": "portfolio_attention.v3",
   "producer": {},
   "inputs": {
     "catalog": {
       "source_id": "portfolio-catalog",
       "sha256": null,
-      "observed_at": "2026-06-15T22:09:43.833784+00:00"
+      "observed_at": "2026-06-16T20:46:39.243078+00:00"
     },
     "workspace": {
       "source_id": "projects-root",
-      "observed_at": "2026-06-15T22:09:43.833784+00:00"
+      "observed_at": "2026-06-16T20:46:39.243078+00:00"
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@@ -21,7 +21,7 @@
     "github_security": {
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       "schema_version": "GitHubSecurityCoverageReceiptV1",
-      "produced_at": "2026-06-15T22:09:43.833784+00:00",
+      "produced_at": "2026-06-16T20:46:39.243078+00:00",
       "state": "fresh",
       "age_hours": 0.0,
       "producer_commit": "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
@@ -89,13 +89,22 @@
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   "exclusions": {
-    "policy_version": "workspace_discovery.v2",
+    "policy_version": "workspace_discovery.v3",
     "counts": {}
   },
   "workspace_root": "/demo-workspace",
   "source_summary": {
     "workspace_root": "/demo-workspace",
     "project_count": 40,
+    "checkout_collisions": {
+      "schema_version": "CheckoutCollisionSummaryV1",
+      "state": "observed",
+      "group_count": 0,
+      "full_clone_group_count": 0,
+      "ambiguous_group_count": 0,
+      "discarded_checkout_count": 0,
+      "groups": []
+    },
     "catalog_errors": [],
     "catalog_warnings": [],
     "legacy_registry_rows": 40,
@@ -297,7 +306,7 @@
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         "next_recommended_move_present": false,
-        "last_meaningful_activity_at": "2025-12-07T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-08T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": true,
         "attention_state": "archived",
@@ -348,7 +357,7 @@
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-        "observed_at": "2026-06-15T22:09:43.833784+00:00",
+        "observed_at": "2026-06-16T20:46:39.243078+00:00",
         "local": {
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           "head": "8adcd37f116d59aaf20b40eaa0cdeab86dfb94991e5a55bc38d5dd9fe605999a",
@@ -486,7 +495,7 @@
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-          "detail": "2025-12-07T22:09:43.833784+00:00"
+          "detail": "2025-12-08T20:46:39.243078+00:00"
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@@ -582,7 +591,7 @@
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         "next_recommended_move_present": false,
-        "last_meaningful_activity_at": "2025-12-07T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-08T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": true,
         "attention_state": "archived",
@@ -633,7 +642,7 @@
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-        "observed_at": "2026-06-15T22:09:43.833784+00:00",
+        "observed_at": "2026-06-16T20:46:39.243078+00:00",
         "local": {
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           "head": "2bde0b8985233649f988ae61d8e1a350bd9b26afe38ba77b1574fc9c7c62ddde",
@@ -771,7 +780,7 @@
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+          "detail": "2025-12-08T20:46:39.243078+00:00"
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@@ -867,7 +876,7 @@
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         "next_recommended_move_present": false,
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+        "last_meaningful_activity_at": "2025-12-08T20:46:39.243078+00:00",
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         "archived": true,
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@@ -918,7 +927,7 @@
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-        "observed_at": "2026-06-15T22:09:43.833784+00:00",
+        "observed_at": "2026-06-16T20:46:39.243078+00:00",
         "local": {
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           "head": "f0dbcdef099e2f12e660a25ffb9724167b98e93d62a073c88ba225ab08c72b01",
@@ -1056,7 +1065,7 @@
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-          "detail": "2025-12-07T22:09:43.833784+00:00"
+          "detail": "2025-12-08T20:46:39.243078+00:00"
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@@ -1152,7 +1161,7 @@
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@@ -1203,7 +1212,7 @@
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-        "observed_at": "2026-06-15T22:09:43.833784+00:00",
+        "observed_at": "2026-06-16T20:46:39.243078+00:00",
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@@ -1341,7 +1350,7 @@
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@@ -1437,7 +1446,7 @@
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-        "last_meaningful_activity_at": "2025-12-07T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-08T20:46:39.243078+00:00",
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@@ -1488,7 +1497,7 @@
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+        "observed_at": "2026-06-16T20:46:39.243078+00:00",
         "local": {
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@@ -1626,7 +1635,7 @@
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+          "detail": "2025-12-08T20:46:39.243078+00:00"
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@@ -1722,7 +1731,7 @@
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+        "last_meaningful_activity_at": "2025-12-08T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": true,
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@@ -1773,7 +1782,7 @@
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-        "observed_at": "2026-06-15T22:09:43.833784+00:00",
+        "observed_at": "2026-06-16T20:46:39.243078+00:00",
         "local": {
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           "head": "2610bee9ecd0d6021c000352f707de6bd4b14266961546fde08835a4501e1f8f",
@@ -1911,7 +1920,7 @@
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+          "detail": "2025-12-08T20:46:39.243078+00:00"
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@@ -2007,7 +2016,7 @@
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-        "last_meaningful_activity_at": "2025-12-07T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-08T20:46:39.243078+00:00",
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@@ -2058,7 +2067,7 @@
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+        "observed_at": "2026-06-16T20:46:39.243078+00:00",
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@@ -2196,7 +2205,7 @@
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+          "detail": "2025-12-08T20:46:39.243078+00:00"
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@@ -2292,7 +2301,7 @@
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-        "last_meaningful_activity_at": "2025-12-07T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-08T20:46:39.243078+00:00",
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@@ -2343,7 +2352,7 @@
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-        "observed_at": "2026-06-15T22:09:43.833784+00:00",
+        "observed_at": "2026-06-16T20:46:39.243078+00:00",
         "local": {
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@@ -2481,7 +2490,7 @@
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@@ -2580,7 +2589,7 @@
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+        "last_meaningful_activity_at": "2026-06-14T20:46:39.243078+00:00",
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@@ -2611,7 +2620,7 @@
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-        "source_produced_at": "2026-06-15T22:09:43.833784+00:00",
+        "source_produced_at": "2026-06-16T20:46:39.243078+00:00",
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@@ -2626,7 +2635,7 @@
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@@ -2649,7 +2658,7 @@
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@@ -2672,7 +2681,7 @@
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@@ -2700,7 +2709,7 @@
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+        "observed_at": "2026-06-16T20:46:39.243078+00:00",
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@@ -2719,7 +2728,7 @@
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+          "observed_at": "2026-06-16T20:46:39.243078+00:00",
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@@ -2846,7 +2855,7 @@
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@@ -2944,7 +2953,7 @@
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+        "last_meaningful_activity_at": "2026-06-14T20:46:39.243078+00:00",
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@@ -2975,7 +2984,7 @@
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-        "source_produced_at": "2026-06-15T22:09:43.833784+00:00",
+        "source_produced_at": "2026-06-16T20:46:39.243078+00:00",
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@@ -2990,7 +2999,7 @@
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@@ -3013,7 +3022,7 @@
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@@ -3036,7 +3045,7 @@
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@@ -3064,7 +3073,7 @@
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+        "observed_at": "2026-06-16T20:46:39.243078+00:00",
         "local": {
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@@ -3083,7 +3092,7 @@
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@@ -3210,7 +3219,7 @@
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@@ -3307,7 +3316,7 @@
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+        "last_meaningful_activity_at": "2026-06-14T20:46:39.243078+00:00",
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@@ -3338,7 +3347,7 @@
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@@ -3353,7 +3362,7 @@
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@@ -3376,7 +3385,7 @@
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@@ -3399,7 +3408,7 @@
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@@ -3427,7 +3436,7 @@
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+        "observed_at": "2026-06-16T20:46:39.243078+00:00",
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@@ -12967,7 +12976,7 @@
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-          "detail": "2025-12-07T22:09:43.833784+00:00"
+          "detail": "2025-12-08T20:46:39.243078+00:00"
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diff --git a/output/demo/portfolio-truth-history-03.json b/output/demo/portfolio-truth-history-03.json
index 40e8636f..d4bb10e0 100644
--- a/output/demo/portfolio-truth-history-03.json
+++ b/output/demo/portfolio-truth-history-03.json
@@ -1,17 +1,17 @@
 {
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-  "generated_at": "2026-06-22T22:09:43.833784+00:00",
+  "generated_at": "2026-06-23T20:46:39.243078+00:00",
   "derivation_policy_version": "portfolio_attention.v3",
   "producer": {},
   "inputs": {
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       "sha256": null,
-      "observed_at": "2026-06-22T22:09:43.833784+00:00"
+      "observed_at": "2026-06-23T20:46:39.243078+00:00"
     },
     "workspace": {
       "source_id": "projects-root",
-      "observed_at": "2026-06-22T22:09:43.833784+00:00"
+      "observed_at": "2026-06-23T20:46:39.243078+00:00"
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@@ -21,7 +21,7 @@
     "github_security": {
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       "schema_version": "GitHubSecurityCoverageReceiptV1",
-      "produced_at": "2026-06-22T22:09:43.833784+00:00",
+      "produced_at": "2026-06-23T20:46:39.243078+00:00",
       "state": "fresh",
       "age_hours": 0.0,
       "producer_commit": "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
@@ -89,13 +89,22 @@
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-    "policy_version": "workspace_discovery.v2",
+    "policy_version": "workspace_discovery.v3",
     "counts": {}
   },
   "workspace_root": "/demo-workspace",
   "source_summary": {
     "workspace_root": "/demo-workspace",
     "project_count": 40,
+    "checkout_collisions": {
+      "schema_version": "CheckoutCollisionSummaryV1",
+      "state": "observed",
+      "group_count": 0,
+      "full_clone_group_count": 0,
+      "ambiguous_group_count": 0,
+      "discarded_checkout_count": 0,
+      "groups": []
+    },
     "catalog_errors": [],
     "catalog_warnings": [],
     "legacy_registry_rows": 40,
@@ -297,7 +306,7 @@
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-        "last_meaningful_activity_at": "2025-12-14T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-15T20:46:39.243078+00:00",
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@@ -348,7 +357,7 @@
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+        "observed_at": "2026-06-23T20:46:39.243078+00:00",
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@@ -486,7 +495,7 @@
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+          "detail": "2025-12-15T20:46:39.243078+00:00"
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@@ -582,7 +591,7 @@
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-        "last_meaningful_activity_at": "2025-12-14T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-15T20:46:39.243078+00:00",
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@@ -633,7 +642,7 @@
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+        "observed_at": "2026-06-23T20:46:39.243078+00:00",
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@@ -771,7 +780,7 @@
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@@ -867,7 +876,7 @@
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@@ -918,7 +927,7 @@
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+        "observed_at": "2026-06-23T20:46:39.243078+00:00",
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@@ -1056,7 +1065,7 @@
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@@ -1152,7 +1161,7 @@
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@@ -1203,7 +1212,7 @@
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+        "observed_at": "2026-06-23T20:46:39.243078+00:00",
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@@ -1341,7 +1350,7 @@
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@@ -1437,7 +1446,7 @@
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@@ -1488,7 +1497,7 @@
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+        "observed_at": "2026-06-23T20:46:39.243078+00:00",
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@@ -1626,7 +1635,7 @@
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@@ -1722,7 +1731,7 @@
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+        "last_meaningful_activity_at": "2025-12-15T20:46:39.243078+00:00",
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@@ -1773,7 +1782,7 @@
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+        "observed_at": "2026-06-23T20:46:39.243078+00:00",
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@@ -1911,7 +1920,7 @@
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@@ -2007,7 +2016,7 @@
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+        "last_meaningful_activity_at": "2025-12-15T20:46:39.243078+00:00",
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@@ -2058,7 +2067,7 @@
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+        "observed_at": "2026-06-23T20:46:39.243078+00:00",
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@@ -2196,7 +2205,7 @@
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@@ -2292,7 +2301,7 @@
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-        "last_meaningful_activity_at": "2025-12-14T22:09:43.833784+00:00",
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@@ -2343,7 +2352,7 @@
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+        "observed_at": "2026-06-23T20:46:39.243078+00:00",
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@@ -2481,7 +2490,7 @@
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@@ -2580,7 +2589,7 @@
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@@ -2611,7 +2620,7 @@
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-        "source_produced_at": "2026-06-22T22:09:43.833784+00:00",
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@@ -2626,7 +2635,7 @@
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@@ -2649,7 +2658,7 @@
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@@ -2672,7 +2681,7 @@
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@@ -2700,7 +2709,7 @@
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@@ -2719,7 +2728,7 @@
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@@ -2846,7 +2855,7 @@
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@@ -2944,7 +2953,7 @@
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@@ -2975,7 +2984,7 @@
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@@ -2990,7 +2999,7 @@
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@@ -3013,7 +3022,7 @@
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@@ -3036,7 +3045,7 @@
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@@ -3064,7 +3073,7 @@
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@@ -3210,7 +3219,7 @@
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@@ -3307,7 +3316,7 @@
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@@ -3338,7 +3347,7 @@
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@@ -3353,7 +3362,7 @@
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@@ -3376,7 +3385,7 @@
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@@ -3399,7 +3408,7 @@
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@@ -3427,7 +3436,7 @@
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@@ -3446,7 +3455,7 @@
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diff --git a/output/demo/portfolio-truth-history-04.json b/output/demo/portfolio-truth-history-04.json
index 5c91bd45..e3b7b943 100644
--- a/output/demo/portfolio-truth-history-04.json
+++ b/output/demo/portfolio-truth-history-04.json
@@ -1,17 +1,17 @@
 {
   "schema_version": "0.11.0",
-  "generated_at": "2026-06-29T22:09:43.833784+00:00",
+  "generated_at": "2026-06-30T20:46:39.243078+00:00",
   "derivation_policy_version": "portfolio_attention.v3",
   "producer": {},
   "inputs": {
     "catalog": {
       "source_id": "portfolio-catalog",
       "sha256": null,
-      "observed_at": "2026-06-29T22:09:43.833784+00:00"
+      "observed_at": "2026-06-30T20:46:39.243078+00:00"
     },
     "workspace": {
       "source_id": "projects-root",
-      "observed_at": "2026-06-29T22:09:43.833784+00:00"
+      "observed_at": "2026-06-30T20:46:39.243078+00:00"
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@@ -21,7 +21,7 @@
     "github_security": {
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       "schema_version": "GitHubSecurityCoverageReceiptV1",
-      "produced_at": "2026-06-29T22:09:43.833784+00:00",
+      "produced_at": "2026-06-30T20:46:39.243078+00:00",
       "state": "fresh",
       "age_hours": 0.0,
       "producer_commit": "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
@@ -89,13 +89,22 @@
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   "exclusions": {
-    "policy_version": "workspace_discovery.v2",
+    "policy_version": "workspace_discovery.v3",
     "counts": {}
   },
   "workspace_root": "/demo-workspace",
   "source_summary": {
     "workspace_root": "/demo-workspace",
     "project_count": 40,
+    "checkout_collisions": {
+      "schema_version": "CheckoutCollisionSummaryV1",
+      "state": "observed",
+      "group_count": 0,
+      "full_clone_group_count": 0,
+      "ambiguous_group_count": 0,
+      "discarded_checkout_count": 0,
+      "groups": []
+    },
     "catalog_errors": [],
     "catalog_warnings": [],
     "legacy_registry_rows": 40,
@@ -297,7 +306,7 @@
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-        "last_meaningful_activity_at": "2025-12-21T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-22T20:46:39.243078+00:00",
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@@ -348,7 +357,7 @@
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+        "observed_at": "2026-06-30T20:46:39.243078+00:00",
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@@ -486,7 +495,7 @@
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+          "detail": "2025-12-22T20:46:39.243078+00:00"
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@@ -582,7 +591,7 @@
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-        "last_meaningful_activity_at": "2025-12-21T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-22T20:46:39.243078+00:00",
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@@ -633,7 +642,7 @@
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+        "observed_at": "2026-06-30T20:46:39.243078+00:00",
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@@ -771,7 +780,7 @@
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+          "detail": "2025-12-22T20:46:39.243078+00:00"
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@@ -867,7 +876,7 @@
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+        "last_meaningful_activity_at": "2025-12-22T20:46:39.243078+00:00",
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@@ -918,7 +927,7 @@
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-        "observed_at": "2026-06-29T22:09:43.833784+00:00",
+        "observed_at": "2026-06-30T20:46:39.243078+00:00",
         "local": {
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@@ -1056,7 +1065,7 @@
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@@ -1152,7 +1161,7 @@
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@@ -1203,7 +1212,7 @@
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+        "observed_at": "2026-06-30T20:46:39.243078+00:00",
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@@ -1341,7 +1350,7 @@
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@@ -1437,7 +1446,7 @@
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-        "last_meaningful_activity_at": "2025-12-21T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-22T20:46:39.243078+00:00",
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@@ -1488,7 +1497,7 @@
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+        "observed_at": "2026-06-30T20:46:39.243078+00:00",
         "local": {
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@@ -1626,7 +1635,7 @@
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@@ -1722,7 +1731,7 @@
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+        "last_meaningful_activity_at": "2025-12-22T20:46:39.243078+00:00",
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@@ -1773,7 +1782,7 @@
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+        "observed_at": "2026-06-30T20:46:39.243078+00:00",
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@@ -1911,7 +1920,7 @@
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+          "detail": "2025-12-22T20:46:39.243078+00:00"
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@@ -2007,7 +2016,7 @@
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-        "last_meaningful_activity_at": "2025-12-21T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-22T20:46:39.243078+00:00",
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@@ -2058,7 +2067,7 @@
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+        "observed_at": "2026-06-30T20:46:39.243078+00:00",
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@@ -2196,7 +2205,7 @@
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@@ -2292,7 +2301,7 @@
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-        "last_meaningful_activity_at": "2025-12-21T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2025-12-22T20:46:39.243078+00:00",
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@@ -2343,7 +2352,7 @@
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+        "observed_at": "2026-06-30T20:46:39.243078+00:00",
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@@ -2481,7 +2490,7 @@
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@@ -2580,7 +2589,7 @@
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@@ -2611,7 +2620,7 @@
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-        "source_produced_at": "2026-06-29T22:09:43.833784+00:00",
+        "source_produced_at": "2026-06-30T20:46:39.243078+00:00",
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@@ -2626,7 +2635,7 @@
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@@ -2649,7 +2658,7 @@
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@@ -2672,7 +2681,7 @@
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@@ -2700,7 +2709,7 @@
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+        "observed_at": "2026-06-30T20:46:39.243078+00:00",
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@@ -2719,7 +2728,7 @@
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@@ -2846,7 +2855,7 @@
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@@ -2944,7 +2953,7 @@
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@@ -2975,7 +2984,7 @@
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+        "source_produced_at": "2026-06-30T20:46:39.243078+00:00",
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@@ -2990,7 +2999,7 @@
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@@ -3013,7 +3022,7 @@
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@@ -3036,7 +3045,7 @@
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@@ -3064,7 +3073,7 @@
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+        "observed_at": "2026-06-30T20:46:39.243078+00:00",
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@@ -3083,7 +3092,7 @@
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@@ -3210,7 +3219,7 @@
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@@ -3307,7 +3316,7 @@
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@@ -3338,7 +3347,7 @@
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@@ -3353,7 +3362,7 @@
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@@ -3376,7 +3385,7 @@
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@@ -3399,7 +3408,7 @@
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@@ -3427,7 +3436,7 @@
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@@ -3446,7 +3455,7 @@
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@@ -3573,7 +3582,7 @@
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@@ -3672,7 +3681,7 @@
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diff --git a/output/demo/portfolio-truth-history-05.json b/output/demo/portfolio-truth-history-05.json
index c3cae4e5..73da5053 100644
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diff --git a/output/demo/portfolio-truth-history-06.json b/output/demo/portfolio-truth-history-06.json
index dc073a29..a36893c4 100644
--- a/output/demo/portfolio-truth-history-06.json
+++ b/output/demo/portfolio-truth-history-06.json
@@ -1,17 +1,17 @@
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+        "observed_at": "2026-07-14T20:46:39.243078+00:00",
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+        "last_meaningful_activity_at": "2026-01-05T20:46:39.243078+00:00",
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+        "observed_at": "2026-07-14T20:46:39.243078+00:00",
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+        "observed_at": "2026-07-14T20:46:39.243078+00:00",
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diff --git a/output/demo/portfolio-truth-history-07.json b/output/demo/portfolio-truth-history-07.json
index 160dec39..6b091d06 100644
--- a/output/demo/portfolio-truth-history-07.json
+++ b/output/demo/portfolio-truth-history-07.json
@@ -1,17 +1,17 @@
 {
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-  "generated_at": "2026-07-20T22:09:43.833784+00:00",
+  "generated_at": "2026-07-21T20:46:39.243078+00:00",
   "derivation_policy_version": "portfolio_attention.v3",
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-      "observed_at": "2026-07-20T22:09:43.833784+00:00"
+      "observed_at": "2026-07-21T20:46:39.243078+00:00"
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-      "observed_at": "2026-07-20T22:09:43.833784+00:00"
+      "observed_at": "2026-07-21T20:46:39.243078+00:00"
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@@ -21,7 +21,7 @@
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       "schema_version": "GitHubSecurityCoverageReceiptV1",
-      "produced_at": "2026-07-20T22:09:43.833784+00:00",
+      "produced_at": "2026-07-21T20:46:39.243078+00:00",
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       "producer_commit": "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
@@ -89,13 +89,22 @@
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-    "policy_version": "workspace_discovery.v2",
+    "policy_version": "workspace_discovery.v3",
     "counts": {}
   },
   "workspace_root": "/demo-workspace",
   "source_summary": {
     "workspace_root": "/demo-workspace",
     "project_count": 40,
+    "checkout_collisions": {
+      "schema_version": "CheckoutCollisionSummaryV1",
+      "state": "observed",
+      "group_count": 0,
+      "full_clone_group_count": 0,
+      "ambiguous_group_count": 0,
+      "discarded_checkout_count": 0,
+      "groups": []
+    },
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     "catalog_warnings": [],
     "legacy_registry_rows": 40,
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diff --git a/output/demo/portfolio-truth-history-08.json b/output/demo/portfolio-truth-history-08.json
index a509d522..bbfc069d 100644
--- a/output/demo/portfolio-truth-history-08.json
+++ b/output/demo/portfolio-truth-history-08.json
@@ -1,17 +1,17 @@
 {
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-  "generated_at": "2026-07-27T22:09:43.833784+00:00",
+  "generated_at": "2026-07-28T20:46:39.243078+00:00",
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+      "observed_at": "2026-07-28T20:46:39.243078+00:00"
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-      "observed_at": "2026-07-27T22:09:43.833784+00:00"
+      "observed_at": "2026-07-28T20:46:39.243078+00:00"
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@@ -21,7 +21,7 @@
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-      "produced_at": "2026-07-27T22:09:43.833784+00:00",
+      "produced_at": "2026-07-28T20:46:39.243078+00:00",
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@@ -89,13 +89,22 @@
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+    "policy_version": "workspace_discovery.v3",
     "counts": {}
   },
   "workspace_root": "/demo-workspace",
   "source_summary": {
     "workspace_root": "/demo-workspace",
     "project_count": 40,
+    "checkout_collisions": {
+      "schema_version": "CheckoutCollisionSummaryV1",
+      "state": "observed",
+      "group_count": 0,
+      "full_clone_group_count": 0,
+      "ambiguous_group_count": 0,
+      "discarded_checkout_count": 0,
+      "groups": []
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     "catalog_warnings": [],
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@@ -11405,7 +11414,7 @@
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@@ -11502,7 +11511,7 @@
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@@ -11531,7 +11540,7 @@
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@@ -11546,7 +11555,7 @@
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+        "observed_at": "2026-07-28T20:46:39.243078+00:00",
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@@ -11759,7 +11768,7 @@
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@@ -11918,7 +11927,7 @@
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@@ -11936,7 +11945,7 @@
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@@ -11962,7 +11971,7 @@
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+        "observed_at": "2026-07-28T20:46:39.243078+00:00",
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@@ -11981,7 +11990,7 @@
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@@ -12105,7 +12114,7 @@
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@@ -12203,7 +12212,7 @@
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+        "last_meaningful_activity_at": "2026-01-19T20:46:39.243078+00:00",
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@@ -12254,7 +12263,7 @@
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+        "observed_at": "2026-07-28T20:46:39.243078+00:00",
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@@ -12392,7 +12401,7 @@
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@@ -12539,7 +12548,7 @@
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+        "observed_at": "2026-07-28T20:46:39.243078+00:00",
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@@ -12677,7 +12686,7 @@
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@@ -12775,7 +12784,7 @@
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@@ -12826,7 +12835,7 @@
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@@ -12964,7 +12973,7 @@
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diff --git a/output/demo/portfolio-truth-history-09.json b/output/demo/portfolio-truth-history-09.json
index 42a0f72b..95e74c75 100644
--- a/output/demo/portfolio-truth-history-09.json
+++ b/output/demo/portfolio-truth-history-09.json
@@ -1,17 +1,17 @@
 {
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-  "generated_at": "2026-08-03T22:09:43.833784+00:00",
+  "generated_at": "2026-08-04T20:46:39.243078+00:00",
   "derivation_policy_version": "portfolio_attention.v3",
   "producer": {},
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       "sha256": null,
-      "observed_at": "2026-08-03T22:09:43.833784+00:00"
+      "observed_at": "2026-08-04T20:46:39.243078+00:00"
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-      "observed_at": "2026-08-03T22:09:43.833784+00:00"
+      "observed_at": "2026-08-04T20:46:39.243078+00:00"
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@@ -21,7 +21,7 @@
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       "schema_version": "GitHubSecurityCoverageReceiptV1",
-      "produced_at": "2026-08-03T22:09:43.833784+00:00",
+      "produced_at": "2026-08-04T20:46:39.243078+00:00",
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       "producer_commit": "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
@@ -89,13 +89,22 @@
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-    "policy_version": "workspace_discovery.v2",
+    "policy_version": "workspace_discovery.v3",
     "counts": {}
   },
   "workspace_root": "/demo-workspace",
   "source_summary": {
     "workspace_root": "/demo-workspace",
     "project_count": 40,
+    "checkout_collisions": {
+      "schema_version": "CheckoutCollisionSummaryV1",
+      "state": "observed",
+      "group_count": 0,
+      "full_clone_group_count": 0,
+      "ambiguous_group_count": 0,
+      "discarded_checkout_count": 0,
+      "groups": []
+    },
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     "catalog_warnings": [],
     "legacy_registry_rows": 40,
@@ -299,7 +308,7 @@
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+        "last_meaningful_activity_at": "2026-01-26T20:46:39.243078+00:00",
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@@ -350,7 +359,7 @@
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+        "observed_at": "2026-08-04T20:46:39.243078+00:00",
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@@ -488,7 +497,7 @@
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@@ -584,7 +593,7 @@
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@@ -11046,7 +11055,7 @@
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@@ -11255,7 +11264,7 @@
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+        "observed_at": "2026-08-04T20:46:39.243078+00:00",
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@@ -11274,7 +11283,7 @@
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@@ -11401,7 +11410,7 @@
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-          "detail": "2026-07-13T22:09:43.833784+00:00"
+          "detail": "2026-07-14T20:46:39.243078+00:00"
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@@ -11498,7 +11507,7 @@
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+        "last_meaningful_activity_at": "2026-01-26T20:46:39.243078+00:00",
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@@ -11527,7 +11536,7 @@
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-        "source_produced_at": "2026-08-03T22:09:43.833784+00:00",
+        "source_produced_at": "2026-08-04T20:46:39.243078+00:00",
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@@ -11542,7 +11551,7 @@
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@@ -11565,7 +11574,7 @@
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@@ -11583,7 +11592,7 @@
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@@ -11609,7 +11618,7 @@
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+        "observed_at": "2026-08-04T20:46:39.243078+00:00",
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@@ -11628,7 +11637,7 @@
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+          "observed_at": "2026-08-04T20:46:39.243078+00:00",
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@@ -11755,7 +11764,7 @@
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+          "detail": "2026-01-26T20:46:39.243078+00:00"
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@@ -11852,7 +11861,7 @@
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+        "last_meaningful_activity_at": "2026-01-26T20:46:39.243078+00:00",
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@@ -11881,7 +11890,7 @@
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-        "source_produced_at": "2026-08-02T21:09:43.833784+00:00",
+        "source_produced_at": "2026-08-03T19:46:39.243078+00:00",
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@@ -11896,7 +11905,7 @@
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@@ -11914,7 +11923,7 @@
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@@ -11932,7 +11941,7 @@
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@@ -11958,7 +11967,7 @@
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+        "observed_at": "2026-08-04T20:46:39.243078+00:00",
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@@ -11977,7 +11986,7 @@
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           "reason_code": "stale_observation",
           "reason": "receipt_stale",
-          "observed_at": "2026-08-02T21:09:43.833784+00:00",
+          "observed_at": "2026-08-03T19:46:39.243078+00:00",
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@@ -12101,7 +12110,7 @@
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-          "detail": "2026-01-25T22:09:43.833784+00:00"
+          "detail": "2026-01-26T20:46:39.243078+00:00"
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@@ -12199,7 +12208,7 @@
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         "next_recommended_move_present": true,
-        "last_meaningful_activity_at": "2026-01-25T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2026-01-26T20:46:39.243078+00:00",
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@@ -12250,7 +12259,7 @@
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-        "observed_at": "2026-08-03T22:09:43.833784+00:00",
+        "observed_at": "2026-08-04T20:46:39.243078+00:00",
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@@ -12388,7 +12397,7 @@
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-          "detail": "2026-01-25T22:09:43.833784+00:00"
+          "detail": "2026-01-26T20:46:39.243078+00:00"
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@@ -12484,7 +12493,7 @@
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         "next_recommended_move_present": true,
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+        "last_meaningful_activity_at": "2026-01-26T20:46:39.243078+00:00",
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@@ -12535,7 +12544,7 @@
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+        "observed_at": "2026-08-04T20:46:39.243078+00:00",
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@@ -12673,7 +12682,7 @@
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+          "detail": "2026-01-26T20:46:39.243078+00:00"
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@@ -12771,7 +12780,7 @@
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-        "last_meaningful_activity_at": "2026-01-25T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2026-01-26T20:46:39.243078+00:00",
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@@ -12822,7 +12831,7 @@
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+        "observed_at": "2026-08-04T20:46:39.243078+00:00",
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@@ -12960,7 +12969,7 @@
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diff --git a/output/demo/portfolio-truth-latest.json b/output/demo/portfolio-truth-latest.json
index 42a0f72b..95e74c75 100644
--- a/output/demo/portfolio-truth-latest.json
+++ b/output/demo/portfolio-truth-latest.json
@@ -1,17 +1,17 @@
 {
   "schema_version": "0.11.0",
-  "generated_at": "2026-08-03T22:09:43.833784+00:00",
+  "generated_at": "2026-08-04T20:46:39.243078+00:00",
   "derivation_policy_version": "portfolio_attention.v3",
   "producer": {},
   "inputs": {
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       "source_id": "portfolio-catalog",
       "sha256": null,
-      "observed_at": "2026-08-03T22:09:43.833784+00:00"
+      "observed_at": "2026-08-04T20:46:39.243078+00:00"
     },
     "workspace": {
       "source_id": "projects-root",
-      "observed_at": "2026-08-03T22:09:43.833784+00:00"
+      "observed_at": "2026-08-04T20:46:39.243078+00:00"
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@@ -21,7 +21,7 @@
     "github_security": {
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       "schema_version": "GitHubSecurityCoverageReceiptV1",
-      "produced_at": "2026-08-03T22:09:43.833784+00:00",
+      "produced_at": "2026-08-04T20:46:39.243078+00:00",
       "state": "fresh",
       "age_hours": 0.0,
       "producer_commit": "aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
@@ -89,13 +89,22 @@
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   "exclusions": {
-    "policy_version": "workspace_discovery.v2",
+    "policy_version": "workspace_discovery.v3",
     "counts": {}
   },
   "workspace_root": "/demo-workspace",
   "source_summary": {
     "workspace_root": "/demo-workspace",
     "project_count": 40,
+    "checkout_collisions": {
+      "schema_version": "CheckoutCollisionSummaryV1",
+      "state": "observed",
+      "group_count": 0,
+      "full_clone_group_count": 0,
+      "ambiguous_group_count": 0,
+      "discarded_checkout_count": 0,
+      "groups": []
+    },
     "catalog_errors": [],
     "catalog_warnings": [],
     "legacy_registry_rows": 40,
@@ -299,7 +308,7 @@
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+        "last_meaningful_activity_at": "2026-01-26T20:46:39.243078+00:00",
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@@ -350,7 +359,7 @@
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+        "observed_at": "2026-08-04T20:46:39.243078+00:00",
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@@ -488,7 +497,7 @@
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+          "detail": "2026-01-26T20:46:39.243078+00:00"
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@@ -584,7 +593,7 @@
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+        "last_meaningful_activity_at": "2026-01-26T20:46:39.243078+00:00",
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@@ -635,7 +644,7 @@
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-        "observed_at": "2026-08-03T22:09:43.833784+00:00",
+        "observed_at": "2026-08-04T20:46:39.243078+00:00",
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         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2026-07-13T22:09:43.833784+00:00"
+          "detail": "2026-07-14T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -10782,7 +10791,7 @@
         "run_instructions_present": true,
         "known_risks_present": true,
         "next_recommended_move_present": true,
-        "last_meaningful_activity_at": "2026-08-01T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2026-08-02T20:46:39.243078+00:00",
         "activity_status": "active",
         "archived": false,
         "attention_state": "experiment",
@@ -10811,7 +10820,7 @@
         "cohort_policy": "portfolio-default-attention-v1",
         "receipt_schema_version": "GitHubSecurityCoverageReceiptV1",
         "receipt_state": "fresh",
-        "source_produced_at": "2026-08-03T22:09:43.833784+00:00",
+        "source_produced_at": "2026-08-04T20:46:39.243078+00:00",
         "providers": {
           "dependabot": {
             "state": "observed",
@@ -10826,7 +10835,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-08-03T22:09:43.833784+00:00",
+            "observed_at": "2026-08-04T20:46:39.243078+00:00",
             "pagination_complete": true,
             "counts": {
               "critical": 0,
@@ -10849,7 +10858,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-08-03T22:09:43.833784+00:00",
+            "observed_at": "2026-08-04T20:46:39.243078+00:00",
             "pagination_complete": true,
             "counts": {
               "critical": 0,
@@ -10872,7 +10881,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-08-03T22:09:43.833784+00:00",
+            "observed_at": "2026-08-04T20:46:39.243078+00:00",
             "pagination_complete": true,
             "counts": {
               "open": 0
@@ -10900,7 +10909,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-08-03T22:09:43.833784+00:00",
+        "observed_at": "2026-08-04T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/studio/juniper-kiln",
           "head": "5a26267fed059db4575fa389c1cf7712acc9c5979f16ccdc7affbebcffdeb54c",
@@ -10919,7 +10928,7 @@
           "state": "observed",
           "reason_code": "observed",
           "reason": null,
-          "observed_at": "2026-08-03T22:09:43.833784+00:00",
+          "observed_at": "2026-08-04T20:46:39.243078+00:00",
           "default_branch": "main",
           "head_sha": "5a26267fed059db4575fa389c1cf7712acc9c5979f16ccdc7affbebcffdeb54c",
           "archived": false
@@ -11046,7 +11055,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2026-08-01T22:09:43.833784+00:00"
+          "detail": "2026-08-02T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -11142,7 +11151,7 @@
         "run_instructions_present": true,
         "known_risks_present": true,
         "next_recommended_move_present": true,
-        "last_meaningful_activity_at": "2026-07-13T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2026-07-14T20:46:39.243078+00:00",
         "activity_status": "recent",
         "archived": false,
         "attention_state": "decision-needed",
@@ -11173,7 +11182,7 @@
         "cohort_policy": "portfolio-default-attention-v1",
         "receipt_schema_version": "GitHubSecurityCoverageReceiptV1",
         "receipt_state": "fresh",
-        "source_produced_at": "2026-08-03T22:09:43.833784+00:00",
+        "source_produced_at": "2026-08-04T20:46:39.243078+00:00",
         "providers": {
           "dependabot": {
             "state": "observed",
@@ -11188,7 +11197,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-08-03T22:09:43.833784+00:00",
+            "observed_at": "2026-08-04T20:46:39.243078+00:00",
             "pagination_complete": true,
             "counts": {
               "critical": 0,
@@ -11211,7 +11220,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-08-03T22:09:43.833784+00:00",
+            "observed_at": "2026-08-04T20:46:39.243078+00:00",
             "pagination_complete": false,
             "counts": null,
             "zero_findings": null
@@ -11229,7 +11238,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-08-03T22:09:43.833784+00:00",
+            "observed_at": "2026-08-04T20:46:39.243078+00:00",
             "pagination_complete": false,
             "counts": null,
             "zero_findings": null
@@ -11255,7 +11264,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-08-03T22:09:43.833784+00:00",
+        "observed_at": "2026-08-04T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/studio/kestrel-loom",
           "head": "def1e22cfe8a27746f826754683cb03ed9a56dffacdf8552654a5d7dc026aa4b",
@@ -11274,7 +11283,7 @@
           "state": "observed",
           "reason_code": "observed",
           "reason": null,
-          "observed_at": "2026-08-03T22:09:43.833784+00:00",
+          "observed_at": "2026-08-04T20:46:39.243078+00:00",
           "default_branch": "main",
           "head_sha": "def1e22cfe8a27746f826754683cb03ed9a56dffacdf8552654a5d7dc026aa4b",
           "archived": false
@@ -11401,7 +11410,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2026-07-13T22:09:43.833784+00:00"
+          "detail": "2026-07-14T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -11498,7 +11507,7 @@
         "run_instructions_present": true,
         "known_risks_present": true,
         "next_recommended_move_present": true,
-        "last_meaningful_activity_at": "2026-01-25T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2026-01-26T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": false,
         "attention_state": "parked",
@@ -11527,7 +11536,7 @@
         "cohort_policy": "portfolio-default-attention-v1",
         "receipt_schema_version": "GitHubSecurityCoverageReceiptV1",
         "receipt_state": "fresh",
-        "source_produced_at": "2026-08-03T22:09:43.833784+00:00",
+        "source_produced_at": "2026-08-04T20:46:39.243078+00:00",
         "providers": {
           "dependabot": {
             "state": "observed",
@@ -11542,7 +11551,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-08-03T22:09:43.833784+00:00",
+            "observed_at": "2026-08-04T20:46:39.243078+00:00",
             "pagination_complete": true,
             "counts": {
               "critical": 0,
@@ -11565,7 +11574,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-08-03T22:09:43.833784+00:00",
+            "observed_at": "2026-08-04T20:46:39.243078+00:00",
             "pagination_complete": false,
             "counts": null,
             "zero_findings": null
@@ -11583,7 +11592,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-08-03T22:09:43.833784+00:00",
+            "observed_at": "2026-08-04T20:46:39.243078+00:00",
             "pagination_complete": false,
             "counts": null,
             "zero_findings": null
@@ -11609,7 +11618,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-08-03T22:09:43.833784+00:00",
+        "observed_at": "2026-08-04T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/studio/nimbus-charter",
           "head": "188af92bf3e2774a55bdfb97d15c601b1130142a1efcc145c37237df33afc20b",
@@ -11628,7 +11637,7 @@
           "state": "observed",
           "reason_code": "observed",
           "reason": null,
-          "observed_at": "2026-08-03T22:09:43.833784+00:00",
+          "observed_at": "2026-08-04T20:46:39.243078+00:00",
           "default_branch": "main",
           "head_sha": "188af92bf3e2774a55bdfb97d15c601b1130142a1efcc145c37237df33afc20b",
           "archived": false
@@ -11755,7 +11764,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2026-01-25T22:09:43.833784+00:00"
+          "detail": "2026-01-26T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -11852,7 +11861,7 @@
         "run_instructions_present": true,
         "known_risks_present": true,
         "next_recommended_move_present": true,
-        "last_meaningful_activity_at": "2026-01-25T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2026-01-26T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": false,
         "attention_state": "manual-only",
@@ -11881,7 +11890,7 @@
         "cohort_policy": "portfolio-default-attention-v1",
         "receipt_schema_version": "GitHubSecurityCoverageReceiptV1",
         "receipt_state": "stale",
-        "source_produced_at": "2026-08-02T21:09:43.833784+00:00",
+        "source_produced_at": "2026-08-03T19:46:39.243078+00:00",
         "providers": {
           "dependabot": {
             "state": "stale",
@@ -11896,7 +11905,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-08-02T21:09:43.833784+00:00",
+            "observed_at": "2026-08-03T19:46:39.243078+00:00",
             "pagination_complete": true,
             "counts": null,
             "zero_findings": null
@@ -11914,7 +11923,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-08-02T21:09:43.833784+00:00",
+            "observed_at": "2026-08-03T19:46:39.243078+00:00",
             "pagination_complete": true,
             "counts": null,
             "zero_findings": null
@@ -11932,7 +11941,7 @@
             },
             "etag": null,
             "last_modified": null,
-            "observed_at": "2026-08-02T21:09:43.833784+00:00",
+            "observed_at": "2026-08-03T19:46:39.243078+00:00",
             "pagination_complete": true,
             "counts": null,
             "zero_findings": null
@@ -11958,7 +11967,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-08-03T22:09:43.833784+00:00",
+        "observed_at": "2026-08-04T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/studio/rialto-pennant",
           "head": "44a43057b9f899b01b1549ac4784c57c6ee9ba43424481bd97662a0635a7b651",
@@ -11977,7 +11986,7 @@
           "state": "stale",
           "reason_code": "stale_observation",
           "reason": "receipt_stale",
-          "observed_at": "2026-08-02T21:09:43.833784+00:00",
+          "observed_at": "2026-08-03T19:46:39.243078+00:00",
           "default_branch": null,
           "head_sha": null,
           "archived": null
@@ -12101,7 +12110,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2026-01-25T22:09:43.833784+00:00"
+          "detail": "2026-01-26T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -12199,7 +12208,7 @@
         "run_instructions_present": true,
         "known_risks_present": true,
         "next_recommended_move_present": true,
-        "last_meaningful_activity_at": "2026-01-25T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2026-01-26T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": false,
         "attention_state": "parked",
@@ -12250,7 +12259,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-08-03T22:09:43.833784+00:00",
+        "observed_at": "2026-08-04T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/studio/umbra-trellis",
           "head": "da48454b7c95b5f168f6696f170b02f445ada6b828e138b1ae9c3aded27a592e",
@@ -12388,7 +12397,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2026-01-25T22:09:43.833784+00:00"
+          "detail": "2026-01-26T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -12484,7 +12493,7 @@
         "run_instructions_present": true,
         "known_risks_present": true,
         "next_recommended_move_present": true,
-        "last_meaningful_activity_at": "2026-01-25T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2026-01-26T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": false,
         "attention_state": "parked",
@@ -12535,7 +12544,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-08-03T22:09:43.833784+00:00",
+        "observed_at": "2026-08-04T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/studio/wicker-obelisk",
           "head": "b82ff66969a92f7a5bc3f63f744a2e5dc5caa0b2d6fa4cbe05ee7ff13a7eb0ab",
@@ -12673,7 +12682,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2026-01-25T22:09:43.833784+00:00"
+          "detail": "2026-01-26T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
@@ -12771,7 +12780,7 @@
         "run_instructions_present": true,
         "known_risks_present": true,
         "next_recommended_move_present": true,
-        "last_meaningful_activity_at": "2026-01-25T22:09:43.833784+00:00",
+        "last_meaningful_activity_at": "2026-01-26T20:46:39.243078+00:00",
         "activity_status": "stale",
         "archived": false,
         "attention_state": "parked",
@@ -12822,7 +12831,7 @@
       },
       "repository_state": {
         "state": "observed",
-        "observed_at": "2026-08-03T22:09:43.833784+00:00",
+        "observed_at": "2026-08-04T20:46:39.243078+00:00",
         "local": {
           "path": "/demo-workspace/studio/yarrow-spindle",
           "head": "f618c22516c338789613aa8b2c965c88debc501e1932019921254bd1efc8b012",
@@ -12960,7 +12969,7 @@
         },
         "derived.last_meaningful_activity_at": {
           "source": "demo-fixture",
-          "detail": "2026-01-25T22:09:43.833784+00:00"
+          "detail": "2026-01-26T20:46:39.243078+00:00"
         },
         "derived.next_recommended_move_present": {
           "source": "demo-fixture",
diff --git a/src/app/portfolio_truth.py b/src/app/portfolio_truth.py
index ba717c91..7e9ce7d6 100644
--- a/src/app/portfolio_truth.py
+++ b/src/app/portfolio_truth.py
@@ -160,6 +160,12 @@ def run_portfolio_truth_mode(args: Any) -> None:
         f"(registry {'updated' if result.registry_changed else 'unchanged'}, "
         f"report {'updated' if result.report_changed else 'unchanged'})"
     )
+    print_info(
+        "Checkout authority: "
+        f"{getattr(result, 'checkout_collision_group_count', 0)} same-origin groups, "
+        f"{getattr(result, 'checkout_authority_unknown_count', 0)} UNKNOWN, "
+        f"{getattr(result, 'discarded_checkout_count', 0)} discarded checkouts"
+    )
 
 
 def run_portfolio_context_recovery_mode(args: Any) -> None:
diff --git a/src/automation_workflow.py b/src/automation_workflow.py
index 93dd7b91..55369f51 100644
--- a/src/automation_workflow.py
+++ b/src/automation_workflow.py
@@ -48,6 +48,10 @@
     _suggested_catalog_seed,
     write_managed_context_block,
 )
+from src.portfolio_checkout_authority import (
+    checkout_authority_blocker,
+    checkout_authority_path,
+)
 from src.portfolio_truth_types import PortfolioTruthProject, PortfolioTruthSnapshot
 
 CONTRACT_VERSION = "automation_workflow_v1"
@@ -87,7 +91,13 @@ def build_context_pr_plan(
     precedence order: explicit ``default_branch`` arg, the repo's detected
     default branch, then the portfolio-wide fallback.
     """
-    repo_path = workspace_root / project.identity.path
+    authority_reason = checkout_authority_blocker(
+        project,
+        workspace_root=workspace_root,
+    )
+    if authority_reason:
+        raise AutomationExecutionError(authority_reason)
+    repo_path = workspace_root / checkout_authority_path(project)
     resolved_branch = default_branch or project.identity.default_branch or DEFAULT_DEFAULT_BRANCH
     display = project.identity.display_name
     commit_message = f"docs(context): refresh managed context block for {display}"
@@ -223,6 +233,14 @@ def _dispatch_proposal(
     if project is None:
         return ExecutionResult(proposal.proposal_id, "skipped", "project-not-found")
 
+    if proposal.action_type in {ACTION_CONTEXT_PR, ACTION_CATALOG_SEED}:
+        authority_reason = checkout_authority_blocker(
+            project,
+            workspace_root=workspace_root,
+        )
+        if authority_reason:
+            raise AutomationExecutionError(authority_reason)
+
     if proposal.action_type == ACTION_CONTEXT_PR:
         # A context-PR needs a real GitHub slug for the head/base refs; we never
         # fabricate one from the local display name (decided 2026-06-06).
diff --git a/src/portfolio_automation.py b/src/portfolio_automation.py
index 75cb968f..9c82f09d 100644
--- a/src/portfolio_automation.py
+++ b/src/portfolio_automation.py
@@ -19,6 +19,8 @@
 from dataclasses import dataclass
 from typing import Any
 
+from src.portfolio_checkout_authority import checkout_authority_blocker
+
 CONTRACT_VERSION = "automation_candidates_v1"
 
 # Trust-bar thresholds. Kept as module constants so later phases (proposal
@@ -86,6 +88,9 @@ def evaluate_automation_eligibility(
         blockers.append("path-confidence-not-high")
     if _text(derived.get("context_quality")) not in ELIGIBLE_CONTEXT_QUALITY:
         blockers.append("context-quality-too-weak")
+    authority_reason = checkout_authority_blocker(project)
+    if authority_reason:
+        blockers.append(authority_reason)
     return AutomationEligibility(eligible=not blockers, blockers=tuple(blockers))
 
 
diff --git a/src/portfolio_checkout_authority.py b/src/portfolio_checkout_authority.py
new file mode 100644
index 00000000..28679249
--- /dev/null
+++ b/src/portfolio_checkout_authority.py
@@ -0,0 +1,386 @@
+from __future__ import annotations
+
+import re
+from collections.abc import Mapping
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Any
+
+from src.portfolio_truth_types import CHECKOUT_COLLISION_SCHEMA_VERSION
+
+
+@dataclass(frozen=True)
+class ValidatedCheckoutAuthority:
+    origin: str
+    checkout_count: int
+    full_clone_count: int
+    state: str
+    reason_code: str
+    canonical_project_path: str
+    representative_path: str
+    selected_path: str | None
+    discarded_count: int
+
+
+def validate_checkout_authority_envelope(
+    authority: object,
+    *,
+    identity_path: str | None = None,
+    repo_full_name: str | None = None,
+) -> ValidatedCheckoutAuthority:
+    """Validate the complete CheckoutCollisionV1 group and its path binding."""
+    if not isinstance(authority, Mapping):
+        raise ValueError("Checkout collision group must be an object.")
+    required_group = {
+        "schema_version",
+        "origin",
+        "canonical_project_path",
+        "checkout_count",
+        "full_clone_count",
+        "declared_checkout_paths",
+        "declared_path_evidence",
+        "unresolved_declared_paths",
+        "selection",
+        "checkouts",
+        "discarded_checkouts",
+    }
+    missing = sorted(required_group - authority.keys())
+    if missing:
+        raise ValueError(f"Checkout collision group is missing fields: {missing}")
+    if authority.get("schema_version") != CHECKOUT_COLLISION_SCHEMA_VERSION:
+        raise ValueError("Unexpected checkout collision schema version.")
+
+    origin = authority.get("origin")
+    if not isinstance(origin, str) or not origin.strip():
+        raise ValueError("Checkout collision origin must be non-empty.")
+    if repo_full_name and origin.lower() != repo_full_name.lower():
+        raise ValueError("Checkout collision origin differs from project identity.")
+    canonical_project_path = _require_relative_path(
+        authority.get("canonical_project_path"),
+        "checkout canonical_project_path",
+    )
+    if identity_path is not None and canonical_project_path != identity_path:
+        raise ValueError("Canonical project path differs from collision identity.")
+
+    checkout_count = _require_nonnegative_count(authority, "checkout_count")
+    full_clone_count = _require_nonnegative_count(authority, "full_clone_count")
+    if checkout_count < 1:
+        raise ValueError("Checkout authority groups require at least one checkout.")
+    if not 1 <= full_clone_count <= checkout_count:
+        raise ValueError("Checkout collision full_clone_count is out of range.")
+
+    selection = authority.get("selection")
+    if not isinstance(selection, Mapping):
+        raise ValueError("Checkout collision selection must be an object.")
+    for key in (
+        "state",
+        "reason_code",
+        "reason",
+        "representative_path",
+        "selected_path",
+        "rationale",
+    ):
+        if key not in selection:
+            raise ValueError(f"Checkout collision selection is missing {key}.")
+    state = selection.get("state")
+    if state not in {"selected", "unknown"}:
+        raise ValueError(f"Invalid checkout authority state: {state}")
+    representative_path = _require_relative_path(
+        selection.get("representative_path"),
+        "checkout representative_path",
+    )
+    selected_path = selection.get("selected_path")
+    if state == "unknown":
+        if selected_path is not None:
+            raise ValueError("UNKNOWN checkout authority cannot select a path.")
+    elif selected_path != representative_path:
+        raise ValueError("Selected checkout path must equal the representative path.")
+    for key in ("reason_code", "reason", "rationale"):
+        if not isinstance(selection.get(key), str) or not selection[key].strip():
+            raise ValueError(
+                f"Checkout collision selection {key} must be non-empty."
+            )
+
+    checkouts = authority.get("checkouts")
+    discarded = authority.get("discarded_checkouts")
+    if not isinstance(checkouts, list) or len(checkouts) != checkout_count:
+        raise ValueError("Checkout collision checkouts do not match checkout_count.")
+    if not isinstance(discarded, list):
+        raise ValueError("Discarded checkouts must be a list.")
+    checkout_paths: set[str] = set()
+    representative_count = 0
+    for checkout in checkouts:
+        if not isinstance(checkout, Mapping):
+            raise ValueError("Checkout collision checkout must be an object.")
+        required_checkout = {
+            "path",
+            "state",
+            "relation",
+            "head",
+            "branch",
+            "dirty",
+            "dirty_path_count",
+            "bare",
+        }
+        missing_checkout = sorted(required_checkout - checkout.keys())
+        if missing_checkout:
+            raise ValueError(
+                f"Checkout collision checkout is missing fields: {missing_checkout}"
+            )
+        path = _require_relative_path(checkout.get("path"), "checkout path")
+        if path in checkout_paths:
+            raise ValueError(f"Duplicate checkout collision path: {path}")
+        checkout_paths.add(path)
+        if checkout.get("state") not in {"observed", "unknown"}:
+            raise ValueError("Invalid checkout observation state.")
+        relation = checkout.get("relation")
+        if relation not in {
+            "representative",
+            "linked_worktree",
+            "independent_full_clone",
+        }:
+            raise ValueError("Invalid checkout relation.")
+        representative_count += int(relation == "representative")
+        head = checkout.get("head")
+        if head is not None and not re.fullmatch(
+            r"[0-9a-f]{40}|[0-9a-f]{64}", str(head)
+        ):
+            raise ValueError(f"Malformed checkout head for {path}.")
+        branch = checkout.get("branch")
+        if branch is not None and not isinstance(branch, str):
+            raise ValueError(f"Malformed checkout branch for {path}.")
+        dirty = checkout.get("dirty")
+        if dirty is not None and not isinstance(dirty, bool):
+            raise ValueError(f"Malformed checkout dirty state for {path}.")
+        dirty_count = checkout.get("dirty_path_count")
+        if dirty_count is not None and (
+            isinstance(dirty_count, bool)
+            or not isinstance(dirty_count, int)
+            or dirty_count < 0
+        ):
+            raise ValueError(f"Malformed checkout dirty_path_count for {path}.")
+        bare = checkout.get("bare")
+        if bare is not None and not isinstance(bare, bool):
+            raise ValueError(f"Malformed checkout bare state for {path}.")
+        if checkout.get("state") == "observed" and not isinstance(bare, bool):
+            raise ValueError(f"Observed checkout must declare bare state for {path}.")
+        if state == "selected":
+            if checkout.get("state") != "observed":
+                raise ValueError(
+                    "Selected checkout authority requires complete observations."
+                )
+            if bare is False and (dirty is not False or dirty_count != 0):
+                raise ValueError(
+                    "Selected checkout authority cannot contain local work."
+                )
+
+    representative_checkout = next(
+        (
+            checkout
+            for checkout in checkouts
+            if checkout["path"] == representative_path
+        ),
+        None,
+    )
+    if (
+        representative_count != 1
+        or representative_checkout is None
+        or representative_checkout["relation"] != "representative"
+        or (
+            state == "selected"
+            and (
+                representative_checkout["state"] != "observed"
+                or representative_checkout["bare"] is not False
+            )
+        )
+    ):
+        raise ValueError("Checkout collision requires one observed representative.")
+    expected_discarded = [
+        checkout
+        for checkout in checkouts
+        if checkout["path"] != representative_path
+    ]
+    if discarded != expected_discarded:
+        raise ValueError("Discarded checkout evidence does not match the checkout set.")
+
+    declared_paths = authority.get("declared_checkout_paths")
+    unresolved_paths = authority.get("unresolved_declared_paths")
+    declared_evidence = authority.get("declared_path_evidence")
+    if not isinstance(declared_paths, list) or not isinstance(
+        unresolved_paths, list
+    ):
+        raise ValueError("Declared checkout paths must be lists.")
+    for path in declared_paths + unresolved_paths:
+        _require_relative_path(path, "declared checkout path")
+    if not isinstance(declared_evidence, list):
+        raise ValueError("Declared path evidence must be a list.")
+    for item in declared_evidence:
+        if not isinstance(item, Mapping):
+            raise ValueError("Declared path evidence must be an object.")
+        _require_relative_path(item.get("source_path"), "declared source path")
+        target = _require_relative_path(
+            item.get("target_checkout_path"), "declared target checkout path"
+        )
+        if target not in checkout_paths:
+            raise ValueError("Declared checkout target is not in the collision group.")
+    expected_declared_paths = sorted(
+        {item["target_checkout_path"] for item in declared_evidence},
+        key=str.lower,
+    )
+    if declared_paths != expected_declared_paths:
+        raise ValueError("Declared checkout paths do not match declared path evidence.")
+    topology_failure = (
+        state == "unknown"
+        and selection.get("reason_code") == "worktree_enumeration_failed"
+    )
+    if checkout_count == 1 and not (
+        declared_evidence or unresolved_paths or topology_failure
+    ):
+        raise ValueError(
+            "Single-checkout authority groups require declaration or "
+            "topology-failure evidence."
+        )
+
+    return ValidatedCheckoutAuthority(
+        origin=origin,
+        checkout_count=checkout_count,
+        full_clone_count=full_clone_count,
+        state=str(state),
+        reason_code=str(selection["reason_code"]),
+        canonical_project_path=canonical_project_path,
+        representative_path=representative_path,
+        selected_path=str(selected_path) if selected_path is not None else None,
+        discarded_count=len(discarded),
+    )
+
+
+def _require_nonnegative_count(value: Mapping[str, Any], key: str) -> int:
+    count = value.get(key)
+    if isinstance(count, bool) or not isinstance(count, int) or count < 0:
+        raise ValueError(f"{key} must be a non-negative integer.")
+    return count
+
+
+def _require_relative_path(value: object, label: str) -> str:
+    if not isinstance(value, str) or not value.strip():
+        raise ValueError(f"{label} must be a non-empty string.")
+    path = Path(value)
+    if path.is_absolute() or ".." in path.parts:
+        raise ValueError(f"{label} must stay workspace-relative.")
+    return value
+
+
+def checkout_authority_blocker(
+    project: Any,
+    *,
+    workspace_root: Path | None = None,
+) -> str | None:
+    """Return a stable automation blocker for unresolved checkout authority.
+
+    Legacy inputs without topology evidence keep their existing behavior. Fresh
+    repository topology fails closed when observation is unknown or multiple
+    worktrees lack matching collision authority. Once collision evidence is
+    present, malformed, UNKNOWN, or path-mismatched selection also fails closed.
+    """
+    identity = _project_section(project, "identity")
+    repository_state = _project_section(project, "repository_state")
+    authority = repository_state.get("checkout_authority")
+    if authority is None:
+        return _repository_topology_blocker(repository_state, authority=None)
+    project_path = str(identity.get("path") or "")
+    repo_full_name = str(identity.get("repo_full_name") or "")
+    try:
+        validated = validate_checkout_authority_envelope(
+            authority,
+            identity_path=project_path,
+            repo_full_name=repo_full_name or None,
+        )
+    except ValueError:
+        return "checkout-authority-malformed"
+    if validated.state != "selected":
+        return f"checkout-authority-unknown:{validated.reason_code}"
+    selected_path = validated.selected_path
+    if selected_path is None:
+        return "checkout-authority-malformed"
+
+    if workspace_root is not None:
+        try:
+            resolved_root = workspace_root.resolve()
+            resolved_target = (workspace_root / selected_path).resolve()
+            resolved_target.relative_to(resolved_root)
+        except (OSError, ValueError):
+            return "checkout-authority-path-escape"
+    return _repository_topology_blocker(repository_state, authority=authority)
+
+
+def checkout_authority_path(project: Any) -> str:
+    """Return the selected checkout path while keeping canonical project identity."""
+    identity = _project_section(project, "identity")
+    project_path = str(identity.get("path") or "")
+    repository_state = _project_section(project, "repository_state")
+    authority = repository_state.get("checkout_authority")
+    repo_full_name = str(identity.get("repo_full_name") or "")
+    try:
+        validated = validate_checkout_authority_envelope(
+            authority,
+            identity_path=project_path,
+            repo_full_name=repo_full_name or None,
+        )
+    except ValueError:
+        return project_path
+    if validated.state == "selected" and validated.selected_path is not None:
+        return validated.selected_path
+    return project_path
+
+
+def _repository_topology_blocker(
+    repository_state: Mapping[str, Any],
+    *,
+    authority: Mapping[str, Any] | None,
+) -> str | None:
+    state = str(repository_state.get("state") or "")
+    if state == "unknown":
+        reason_code = str(
+            repository_state.get("reason_code") or "repository_observation_failed"
+        )
+        return f"checkout-topology-unknown:{reason_code}"
+
+    worktrees = repository_state.get("worktrees")
+    if worktrees is None:
+        return None
+    if not isinstance(worktrees, list) or any(
+        not isinstance(item, Mapping) for item in worktrees
+    ):
+        return "checkout-topology-malformed"
+    if len(worktrees) <= 1:
+        return None
+    if authority is None:
+        return "checkout-authority-missing:multiple-worktrees"
+    if any(item.get("state") not in {"observed", "coordinator"} for item in worktrees):
+        return "checkout-topology-unknown:worktree_observation_failed"
+    if any(item.get("dirty") is True for item in worktrees):
+        return "checkout-topology-local-work-present"
+
+    authority_checkouts = authority.get("checkouts")
+    if not isinstance(authority_checkouts, list):
+        return "checkout-authority-malformed"
+    representative_clone_count = sum(
+        isinstance(item, Mapping)
+        and item.get("relation") in {"representative", "linked_worktree"}
+        for item in authority_checkouts
+    )
+    if representative_clone_count != len(worktrees):
+        return "checkout-authority-topology-mismatch"
+    return None
+
+
+def _project_section(project: Any, name: str) -> Mapping[str, Any]:
+    if isinstance(project, Mapping):
+        value = project.get(name)
+    else:
+        value = getattr(project, name, None)
+    if isinstance(value, Mapping):
+        return value
+    if value is not None and hasattr(value, "__dict__"):
+        return vars(value)
+    return {}
diff --git a/src/portfolio_context_recovery.py b/src/portfolio_context_recovery.py
index ee4b3d4b..89b025c7 100644
--- a/src/portfolio_context_recovery.py
+++ b/src/portfolio_context_recovery.py
@@ -16,6 +16,10 @@
     temporary_project_reason,
     upsert_managed_context_block,
 )
+from src.portfolio_checkout_authority import (
+    checkout_authority_blocker,
+    checkout_authority_path,
+)
 from src.portfolio_truth_types import (
     PortfolioTruthProject,
     PortfolioTruthSnapshot,
@@ -86,7 +90,8 @@ def build_context_recovery_plan(
     target_projects.sort(key=_recovery_priority)
 
     for index, project in enumerate(target_projects, start=1):
-        project_path = workspace_root / project.identity.path
+        execution_path = checkout_authority_path(project)
+        project_path = workspace_root / execution_path
         reason = temporary_project_reason(
             project.identity.project_key, project.identity.display_name
         )
@@ -94,13 +99,21 @@ def build_context_recovery_plan(
         if reason:
             status = "excluded"
         else:
+            authority_reason = checkout_authority_blocker(
+                project,
+                workspace_root=workspace_root,
+            )
+            if authority_reason:
+                status = "skipped"
+                reason = authority_reason
             if not allow_dirty:
-                dirty_reason = _dirty_worktree_reason(
-                    project_path, project.identity.has_git
-                )
-                if dirty_reason:
-                    status = "skipped"
-                    reason = dirty_reason
+                if status == "eligible":
+                    dirty_reason = _dirty_worktree_reason(
+                        project_path, project.identity.has_git
+                    )
+                    if dirty_reason:
+                        status = "skipped"
+                        reason = dirty_reason
             if status == "eligible":
                 ambiguous_reason = _ambiguous_primary_context_reason(project_path)
                 if ambiguous_reason:
@@ -112,7 +125,7 @@ def build_context_recovery_plan(
                 priority_rank=index,
                 project_key=project.identity.project_key,
                 display_name=project.identity.display_name,
-                relative_path=project.identity.path,
+                relative_path=execution_path,
                 activity_status=display_activity_status(
                     project.derived.activity_status, archived=project.derived.archived
                 ),
@@ -193,8 +206,14 @@ def apply_context_recovery_plan(
 
     for target in eligible_targets:
         project = project_index[target.project_key]
-        project_path = workspace_root / project.identity.path
+        project_path = workspace_root / checkout_authority_path(project)
         try:
+            authority_reason = checkout_authority_blocker(
+                project,
+                workspace_root=workspace_root,
+            )
+            if authority_reason:
+                raise RuntimeError(authority_reason)
             write_managed_context_block(project, project_path)
             updated.append(target.project_key)
             if target.suggested_catalog_seed:
diff --git a/src/portfolio_repository_state.py b/src/portfolio_repository_state.py
index adbbd6a9..571f8882 100644
--- a/src/portfolio_repository_state.py
+++ b/src/portfolio_repository_state.py
@@ -14,6 +14,7 @@ def observe_repository_state(
     *,
     observed_at: datetime,
     remote_default_branch: dict[str, Any] | None = None,
+    workspace_root: Path | None = None,
 ) -> dict[str, Any]:
     """Read local Git/worktree state without changing refs or exposing file names."""
     remote = (
@@ -36,7 +37,7 @@ def observe_repository_state(
         }
 
     try:
-        worktrees = _observe_worktrees(path)
+        worktrees = _observe_worktrees(path, workspace_root=workspace_root)
         selection = _select_remote_default_worktree(worktrees, remote)
         topology = {
             "kind": repository_kind,
@@ -204,10 +205,39 @@ def _observe_bare_coordinator(path: Path) -> dict[str, Any]:
     }
 
 
-def _observe_worktrees(path: Path) -> list[dict[str, Any]]:
+def _observe_worktrees(
+    path: Path, *, workspace_root: Path | None = None
+) -> list[dict[str, Any]]:
     observed: list[dict[str, Any]] = []
+    external_worktree_count = 0
     for item in _worktrees(path):
         worktree_path = Path(item["path"])
+        if workspace_root is not None and not _path_is_within(
+            worktree_path, workspace_root
+        ):
+            external_worktree_count += 1
+            opaque_path = (
+                "external-worktree"
+                if external_worktree_count == 1
+                else f"external-worktree-{external_worktree_count}"
+            )
+            observed.append(
+                {
+                    "state": "unknown",
+                    "reason_code": "external_worktree_outside_workspace",
+                    "reason": (
+                        "the linked worktree is outside the observed workspace"
+                    ),
+                    "path": opaque_path,
+                    "head": None,
+                    "branch": None,
+                    "detached": False,
+                    "bare": bool(item.get("bare")),
+                    "dirty": None,
+                    "dirty_path_count": None,
+                }
+            )
+            continue
         if item.get("bare"):
             observed.append(
                 {
@@ -251,6 +281,14 @@ def _observe_worktrees(path: Path) -> list[dict[str, Any]]:
     return observed
 
 
+def _path_is_within(candidate: Path, root: Path) -> bool:
+    try:
+        candidate.resolve().relative_to(root.resolve())
+        return True
+    except (OSError, ValueError):
+        return False
+
+
 def _select_remote_default_worktree(
     worktrees: list[dict[str, Any]], remote: dict[str, Any]
 ) -> dict[str, Any]:
diff --git a/src/portfolio_truth_metadata.py b/src/portfolio_truth_metadata.py
index a8129c86..06a6c88f 100644
--- a/src/portfolio_truth_metadata.py
+++ b/src/portfolio_truth_metadata.py
@@ -10,7 +10,10 @@
 from typing import Any
 
 from src.portfolio_truth_coverage import ProjectLike
-from src.portfolio_truth_sources import WORKSPACE_DISCOVERY_POLICY_VERSION
+from src.portfolio_truth_sources import (
+    WORKSPACE_DISCOVERY_POLICY_VERSION,
+    checkout_collision_summary,
+)
 
 
 def _section(project: ProjectLike, name: str) -> Any:
@@ -77,11 +80,13 @@ def build_source_summary(
     legacy_registry_rows: int,
     notion_context_rows: int,
     notion_context_carried_forward: bool,
+    checkout_collisions: Sequence[dict[str, Any]] = (),
 ) -> dict[str, Any]:
     """Build the exact producer summary from bounded inputs and project facts."""
     return {
         "workspace_root": workspace_root,
         "project_count": len(projects),
+        "checkout_collisions": checkout_collision_summary(list(checkout_collisions)),
         "catalog_errors": list(catalog_errors),
         "catalog_warnings": list(catalog_warnings),
         "legacy_registry_rows": legacy_registry_rows,
@@ -130,6 +135,7 @@ def build_warnings(
     catalog_errors: Sequence[str],
     catalog_warnings: Sequence[str],
     unresolved_duplicates: Sequence[str],
+    checkout_collisions: Sequence[dict[str, Any]] = (),
 ) -> list[str]:
     warnings = [*catalog_errors, *catalog_warnings]
     if unresolved_duplicates:
@@ -137,6 +143,16 @@ def build_warnings(
             "Duplicate project display names require path-qualified registry labels: "
             + ", ".join(unresolved_duplicates)
         )
+    ambiguous_checkout_origins = [
+        str(group["origin"])
+        for group in checkout_collisions
+        if group.get("selection", {}).get("state") == "unknown"
+    ]
+    if ambiguous_checkout_origins:
+        warnings.append(
+            "Checkout authority is UNKNOWN for same-origin checkout groups: "
+            + ", ".join(ambiguous_checkout_origins)
+        )
     return warnings
 
 
diff --git a/src/portfolio_truth_publish.py b/src/portfolio_truth_publish.py
index 25b94e1d..8a68edff 100644
--- a/src/portfolio_truth_publish.py
+++ b/src/portfolio_truth_publish.py
@@ -50,6 +50,9 @@ class PortfolioTruthPublishResult:
     registry_changed: bool
     report_changed: bool
     project_registry_path: Path | None = None
+    checkout_collision_group_count: int = 0
+    checkout_authority_unknown_count: int = 0
+    discarded_checkout_count: int = 0
 
 
 @dataclass(frozen=True)
@@ -530,6 +533,7 @@ def _publish_portfolio_truth_locked(
     for staged in temp_files.values():
         staged.unlink(missing_ok=True)
 
+    collision_summary = build_result.snapshot.source_summary["checkout_collisions"]
     return PortfolioTruthPublishResult(
         snapshot_path=snapshot_path,
         latest_path=latest_path,
@@ -539,6 +543,11 @@ def _publish_portfolio_truth_locked(
         registry_changed=changed[registry_output],
         report_changed=changed[portfolio_report_output],
         project_registry_path=project_registry_path,
+        checkout_collision_group_count=int(collision_summary["group_count"]),
+        checkout_authority_unknown_count=int(
+            collision_summary["ambiguous_group_count"]
+        ),
+        discarded_checkout_count=int(collision_summary["discarded_checkout_count"]),
     )
 
 
diff --git a/src/portfolio_truth_reconcile.py b/src/portfolio_truth_reconcile.py
index 23565497..f7824193 100644
--- a/src/portfolio_truth_reconcile.py
+++ b/src/portfolio_truth_reconcile.py
@@ -419,11 +419,13 @@ def build_portfolio_truth_snapshot(
         )
 
     exclusion_counts: dict[str, int] = {}
+    checkout_collisions: list[dict[str, Any]] = []
     workspace_projects = discover_workspace_projects(
         workspace_root,
         catalog_data=catalog_data,
         now=now,
         exclusion_counts=exclusion_counts,
+        checkout_collisions=checkout_collisions,
     )
     workspace_projects = _merge_supplementary_discoveries(
         discovered=workspace_projects,
@@ -445,6 +447,7 @@ def materialize_projects(
                 legacy_rows=legacy_rows,
                 notion_context=notion_context,
                 now=now,
+                workspace_root=workspace_root,
                 release_count_by_name=release_count_by_name,
                 security_alerts_by_name=security_lookup,
                 repo_status_by_name=repo_status_lookup,
@@ -501,11 +504,13 @@ def materialize_projects(
         legacy_registry_rows=len(legacy_rows),
         notion_context_rows=len(notion_context),
         notion_context_carried_forward=notion_context_carried_forward,
+        checkout_collisions=checkout_collisions,
     )
     warnings = build_warnings(
         catalog_errors=source_summary["catalog_errors"],
         catalog_warnings=source_summary["catalog_warnings"],
         unresolved_duplicates=source_summary["unresolved_duplicate_display_names"],
+        checkout_collisions=checkout_collisions,
     )
 
     snapshot = PortfolioTruthSnapshot(
@@ -793,6 +798,7 @@ def _build_truth_project(
     legacy_rows: dict[str, dict[str, str]],
     notion_context: dict[str, dict[str, str]],
     now: datetime,
+    workspace_root: Path,
     release_count_by_name: dict[str, int] | None = None,
     security_alerts_by_name: dict[str, dict] | None = None,
     repo_status_by_name: dict[str, dict] | None = None,
@@ -1170,6 +1176,7 @@ def _build_truth_project(
             project_path,
             observed_at=now,
             remote_default_branch=remote_default_branch,
+            workspace_root=workspace_root,
         )
         if project_path is not None and has_git
         else {
@@ -1186,6 +1193,12 @@ def _build_truth_project(
             },
         }
     )
+    checkout_authority = raw_project.get("checkout_authority")
+    if isinstance(checkout_authority, dict):
+        repository_state = {
+            **repository_state,
+            "checkout_authority": checkout_authority,
+        }
     return PortfolioTruthProject(
         identity=identity,
         declared=declared,
diff --git a/src/portfolio_truth_render.py b/src/portfolio_truth_render.py
index 06bb5b15..733acd14 100644
--- a/src/portfolio_truth_render.py
+++ b/src/portfolio_truth_render.py
@@ -2,6 +2,7 @@
 
 from collections import Counter, defaultdict
 from datetime import timezone
+from typing import Any
 
 from src.portfolio_truth_types import (
     PortfolioTruthProject,
@@ -132,6 +133,7 @@ def render_portfolio_report_markdown(
     )
     risk_tier_counts = Counter(project.risk.risk_tier for project in snapshot.projects)
     security_overview = _security_overview(snapshot.projects)
+    checkout_collisions = snapshot.source_summary.get("checkout_collisions", {})
     lines = [
         GENERATED_MARKDOWN_PROVENANCE_MARKER,
         "",
@@ -145,13 +147,14 @@ def render_portfolio_report_markdown(
         "## Table of Contents",
         "",
         "1. [Portfolio truth summary](#portfolio-truth-summary)",
-        "2. [Audit Methodology](#audit-methodology)",
-        "3. [Canonical Portfolio Truth Table](#canonical-portfolio-truth-table)",
-        "4. [Coverage Summary](#coverage-summary)",
-        "5. [Breakdown by Portfolio Signals](#breakdown-by-portfolio-signals)",
-        "6. [Security Posture](#security-posture)",
-        "7. [Accuracy Findings](#accuracy-findings)",
-        "8. [Recommended Next Sync Steps](#recommended-next-sync-steps)",
+        "2. [Checkout Authority](#checkout-authority)",
+        "3. [Audit Methodology](#audit-methodology)",
+        "4. [Canonical Portfolio Truth Table](#canonical-portfolio-truth-table)",
+        "5. [Coverage Summary](#coverage-summary)",
+        "6. [Breakdown by Portfolio Signals](#breakdown-by-portfolio-signals)",
+        "7. [Security Posture](#security-posture)",
+        "8. [Accuracy Findings](#accuracy-findings)",
+        "9. [Recommended Next Sync Steps](#recommended-next-sync-steps)",
         "",
         "---",
         "",
@@ -163,6 +166,8 @@ def render_portfolio_report_markdown(
         f"- Grouped sections represented: `{len(grouped)}`",
         f"- Canonical source path: `{latest_json_path}`",
         "",
+        *_render_checkout_authority_section(checkout_collisions),
+        "",
         "## Audit Methodology",
         "",
         "- The truth layer scans the local workspace first, using directory metadata and small allowlisted context files only.",
@@ -293,6 +298,67 @@ def render_portfolio_report_markdown(
     return "\n".join(lines) + "\n"
 
 
+def _render_checkout_authority_section(summary: dict[str, Any]) -> list[str]:
+    group_count = summary.get("group_count", 0)
+    ambiguous_count = summary.get("ambiguous_group_count", 0)
+    discarded_count = summary.get("discarded_checkout_count", 0)
+    lines = [
+        "## Checkout Authority",
+        "",
+        f"- Same-origin checkout groups: `{group_count}`",
+        f"- Authority state UNKNOWN: `{ambiguous_count}`",
+        f"- Discarded checkout records retained: `{discarded_count}`",
+        "- Selection policy: preserve one compatibility representative per origin; "
+        + "independent full-clone conflicts remain UNKNOWN.",
+    ]
+    groups = summary.get("groups", [])
+    if not groups:
+        lines.append("- No same-origin checkout collisions were observed.")
+        return lines
+
+    lines.extend(
+        [
+            "",
+            "| Origin | Authority | Representative | Selected checkout | Discarded | Reason |",
+            "|--------|-----------|----------------|-------------------|-----------|--------|",
+        ]
+    )
+    for group in groups:
+        selection = group["selection"]
+        selected = selection.get("selected_path") or "UNKNOWN"
+        lines.append(
+            f"| `{group['origin']}` | {selection['state']} | "
+            f"`{selection['representative_path']}` | `{selected}` | "
+            f"{len(group['discarded_checkouts'])} | "
+            f"`{selection['reason_code']}` |"
+        )
+
+    lines.extend(["", "### Discarded Checkout Evidence", ""])
+    for group in groups:
+        selection = group["selection"]
+        lines.append(f"- `{group['origin']}` selection: {selection['reason']}")
+        for checkout in group["discarded_checkouts"]:
+            head = checkout.get("head") or "UNKNOWN"
+            branch = checkout.get("branch") or "detached-or-UNKNOWN"
+            if checkout.get("dirty") is True:
+                dirty = f"dirty ({checkout['dirty_path_count']} paths)"
+            elif checkout.get("dirty") is False:
+                dirty = "clean"
+            else:
+                dirty = "dirty state UNKNOWN"
+            lines.append(
+                f"  - `{checkout['path']}`: `{checkout['relation']}`, "
+                f"head `{head}`, branch `{branch}`, {dirty}."
+            )
+        if group.get("declared_checkout_paths"):
+            paths = "`, `".join(group["declared_checkout_paths"])
+            lines.append(f"  - Declared checkout paths resolve to: `{paths}`.")
+        if group.get("unresolved_declared_paths"):
+            paths = "`, `".join(group["unresolved_declared_paths"])
+            lines.append(f"  - Unresolved declared checkout paths: `{paths}`.")
+    return lines
+
+
 def _group_projects(
     projects: list[PortfolioTruthProject],
 ) -> dict[str, list[PortfolioTruthProject]]:
diff --git a/src/portfolio_truth_sources.py b/src/portfolio_truth_sources.py
index 3c78a11d..909b1e5e 100644
--- a/src/portfolio_truth_sources.py
+++ b/src/portfolio_truth_sources.py
@@ -13,6 +13,10 @@
 from src.notion_registry import load_notion_project_context
 from src.portfolio_catalog import group_entry_for_path
 from src.portfolio_context_contract import analyze_project_context
+from src.portfolio_truth_types import (
+    CHECKOUT_COLLISION_SCHEMA_VERSION,
+    CHECKOUT_COLLISION_SUMMARY_SCHEMA_VERSION,
+)
 from src.registry_parser import _normalize
 
 MAX_CONTEXT_DEPTH = 2
@@ -106,7 +110,7 @@
 ARCHIVE_REMOTE_BASENAME_TOKENS = frozenset({"private-archive", "scrubbed-import"})
 
 
-WORKSPACE_DISCOVERY_POLICY_VERSION = "workspace_discovery.v2"
+WORKSPACE_DISCOVERY_POLICY_VERSION = "workspace_discovery.v3"
 WORKSPACE_EXCLUSION_REASONS = frozenset(
     {
         "backup-container",
@@ -122,6 +126,12 @@
 )
 MAX_NOTION_SNAPSHOT_AGE_HOURS = 30
 
+_CANONICAL_PATHS_HEADING = re.compile(
+    r"^(?P<marks>#{1,6})\s+canonical\s+paths?\s*$", re.IGNORECASE
+)
+_MARKDOWN_HEADING = re.compile(r"^(?P<marks>#{1,6})\s+\S")
+_ABSOLUTE_CODE_PATH = re.compile(r"`(?P<path>/[^`\r\n]+)`")
+
 
 class NotionProjectContext(dict[str, dict[str, str]]):
     def __init__(
@@ -173,6 +183,7 @@ def discover_workspace_projects(
     catalog_data: dict[str, Any],
     now: datetime | None = None,
     exclusion_counts: dict[str, int] | None = None,
+    checkout_collisions: list[dict[str, Any]] | None = None,
 ) -> list[dict[str, Any]]:
     discovered: list[dict[str, Any]] = []
     now = now or datetime.now(timezone.utc)
@@ -199,11 +210,22 @@ def discover_workspace_projects(
                 exclusion_counts=exclusion_counts,
             )
         )
-    return _dedupe_checkouts_by_origin(discovered)
+    return _dedupe_checkouts_by_origin(
+        discovered,
+        checkout_collisions=checkout_collisions,
+        workspace_root=workspace_root,
+        catalog_data=catalog_data,
+        now=now,
+    )
 
 
 def _dedupe_checkouts_by_origin(
     discovered: list[dict[str, Any]],
+    *,
+    checkout_collisions: list[dict[str, Any]] | None = None,
+    workspace_root: Path | None = None,
+    catalog_data: dict[str, Any] | None = None,
+    now: datetime | None = None,
 ) -> list[dict[str, Any]]:
     """Collapse multiple on-disk checkouts of the same repo to one canonical project.
 
@@ -212,10 +234,11 @@ def _dedupe_checkouts_by_origin(
     (``repo_full_name``), so without this they each count as a distinct project —
     inflating the portfolio count and dragging catalog-completeness toward zero.
 
-    Keep one canonical checkout per origin, preferring the directory whose name
-    matches the repo basename, then the shortest name, then alphabetical. Projects
-    without an origin are local-only and are never collapsed. Result is sorted by
-    name (case-insensitive), matching the prior discovery ordering.
+    Keep one compatibility representative per origin without claiming checkout
+    authority when independent full clones disagree. Every non-representative
+    checkout remains visible in ``CheckoutCollisionV1`` evidence. Projects without
+    an origin are local-only and are never collapsed. Result is sorted by name
+    (case-insensitive), matching the prior discovery ordering.
     """
     by_origin: dict[str, list[dict[str, Any]]] = {}
     canonical: list[dict[str, Any]] = []
@@ -227,22 +250,457 @@ def _dedupe_checkouts_by_origin(
             canonical.append(project)
 
     for origin_key, group in by_origin.items():
-        repo_base = origin_key.rsplit("/", 1)[-1]
-        canonical.append(
-            min(
-                group,
-                key=lambda p: (
-                    str(p.get("name", "")).lower() != repo_base,
-                    len(str(p.get("name", ""))),
-                    str(p.get("name", "")).lower(),
-                ),
-            )
+        identity_project = _checkout_identity_project(group, origin_key)
+        authority_group = _checkout_topology_group(
+            group,
+            workspace_root=workspace_root,
+            catalog_data=catalog_data,
+            now=now,
+        )
+        representative = _checkout_representative(authority_group, origin_key)
+        canonical_project = _canonical_checkout_project(
+            identity_project=identity_project,
+            representative=representative,
         )
+        has_checkout_declarations = any(
+            _checkout_observation(project).get("declared_paths")
+            for project in authority_group
+        )
+        has_topology_failure = any(
+            project.get("_worktree_enumeration_failed") is True
+            for project in authority_group
+        )
+        if (
+            len(authority_group) > 1
+            or has_checkout_declarations
+            or has_topology_failure
+        ):
+            collision = _checkout_collision_record(
+                origin=str(representative.get("repo_full_name") or origin_key),
+                origin_key=origin_key,
+                group=authority_group,
+                representative=representative,
+                canonical_project_path=str(canonical_project.get("path") or ""),
+            )
+            canonical_project["checkout_authority"] = collision
+            if checkout_collisions is not None:
+                checkout_collisions.append(collision)
+        canonical.append(canonical_project)
 
     canonical.sort(key=lambda p: str(p.get("name", "")).lower())
     return canonical
 
 
+def _checkout_topology_group(
+    group: list[dict[str, Any]],
+    *,
+    workspace_root: Path | None,
+    catalog_data: dict[str, Any] | None,
+    now: datetime | None,
+) -> list[dict[str, Any]]:
+    """Add linked worktrees to authority without duplicating logical projects."""
+    if workspace_root is None:
+        return list(group)
+    if catalog_data is None or now is None:
+        raise ValueError("topology expansion requires discovery inputs")
+
+    resolved_root = workspace_root.resolve()
+    expanded = list(group)
+    known_paths = {
+        Path(str(project["project_path"])).resolve() for project in group
+    }
+    published_paths = {str(project.get("path") or "") for project in group}
+    external_worktree_count = 0
+    for source_project in group:
+        project_path = Path(str(source_project["project_path"]))
+        try:
+            worktree_paths = _git_worktree_paths(project_path)
+        except (
+            OSError,
+            ValueError,
+            subprocess.CalledProcessError,
+            subprocess.TimeoutExpired,
+        ):
+            source_project["_worktree_enumeration_failed"] = True
+            continue
+        for worktree_path in worktree_paths:
+            resolved_path = worktree_path.resolve()
+            if resolved_path in known_paths:
+                continue
+            known_paths.add(resolved_path)
+            if not _path_is_within(resolved_path, resolved_root):
+                external_worktree_count += 1
+                opaque_path = (
+                    "external-worktree"
+                    if external_worktree_count == 1
+                    else f"external-worktree-{external_worktree_count}"
+                )
+                while opaque_path in published_paths:
+                    external_worktree_count += 1
+                    opaque_path = f"external-worktree-{external_worktree_count}"
+                published_paths.add(opaque_path)
+                source_observation = _checkout_observation(source_project)
+                expanded.append(
+                    {
+                        "name": opaque_path,
+                        "path": opaque_path,
+                        "project_path": resolved_root / opaque_path,
+                        "repo_full_name": source_project.get("repo_full_name", ""),
+                        "_external_worktree": True,
+                        "_checkout_observation": {
+                            "state": "unknown",
+                            "head": None,
+                            "branch": None,
+                            "dirty": None,
+                            "dirty_path_count": None,
+                            "git_common_dir": source_observation.get("git_common_dir"),
+                            "bare": None,
+                            "declared_paths": [],
+                        },
+                    }
+                )
+                continue
+            try:
+                linked_project = _inspect_project_dir(
+                    resolved_path,
+                    resolved_root,
+                    catalog_data=catalog_data,
+                    now=now,
+                )
+            except OSError:
+                linked_project = {
+                    "name": resolved_path.name,
+                    "path": resolved_path.relative_to(resolved_root).as_posix(),
+                    "project_path": resolved_path,
+                    "_checkout_observation": _checkout_observation({}),
+                }
+            linked_project["repo_full_name"] = source_project.get("repo_full_name", "")
+            expanded.append(linked_project)
+    return expanded
+
+
+def _git_worktree_paths(project_path: Path) -> list[Path]:
+    output = _git_read(project_path, "worktree", "list", "--porcelain")
+    paths = [
+        Path(line.removeprefix("worktree "))
+        for line in output.splitlines()
+        if line.startswith("worktree ")
+    ]
+    if not paths:
+        raise ValueError("git worktree list returned no worktrees")
+    return paths
+
+
+def checkout_collision_summary(
+    collisions: list[dict[str, Any]],
+) -> dict[str, Any]:
+    """Build the stable portfolio-level collision summary without adding projects."""
+    groups = sorted(collisions, key=lambda item: str(item["origin"]).lower())
+    ambiguous_group_count = sum(
+        item["selection"]["state"] == "unknown" for item in groups
+    )
+    return {
+        "schema_version": CHECKOUT_COLLISION_SUMMARY_SCHEMA_VERSION,
+        "state": "unknown" if ambiguous_group_count else "observed",
+        "group_count": len(groups),
+        "full_clone_group_count": sum(
+            int(item["full_clone_count"] > 1) for item in groups
+        ),
+        "ambiguous_group_count": ambiguous_group_count,
+        "discarded_checkout_count": sum(
+            len(item["discarded_checkouts"]) for item in groups
+        ),
+        "groups": groups,
+    }
+
+
+def _checkout_representative(
+    group: list[dict[str, Any]], origin_key: str
+) -> dict[str, Any]:
+    repo_base = origin_key.rsplit("/", 1)[-1]
+    return min(
+        group,
+        key=lambda project: (
+            _checkout_observation(project).get("state") != "observed",
+            _checkout_observation(project).get("bare") is True,
+            str(project.get("name", "")).lower() != repo_base,
+            len(Path(str(project.get("path", ""))).parts),
+            len(str(project.get("path", ""))),
+            str(project.get("path", "")).lower(),
+        ),
+    )
+
+
+def _checkout_identity_project(
+    group: list[dict[str, Any]], origin_key: str
+) -> dict[str, Any]:
+    """Choose stable catalog identity independently of mutation-path health."""
+    repo_base = origin_key.rsplit("/", 1)[-1]
+    return min(
+        group,
+        key=lambda project: (
+            str(project.get("name", "")).lower() != repo_base,
+            len(Path(str(project.get("path", ""))).parts),
+            len(str(project.get("path", ""))),
+            str(project.get("path", "")).lower(),
+        ),
+    )
+
+
+def _canonical_checkout_project(
+    *,
+    identity_project: dict[str, Any],
+    representative: dict[str, Any],
+) -> dict[str, Any]:
+    """Keep discovered identity while observing the selected healthy checkout."""
+    if identity_project is representative:
+        return representative
+    canonical = dict(representative)
+    for key in ("name", "path", "top_level_dir", "group_entry", "source"):
+        if key in identity_project:
+            canonical[key] = identity_project[key]
+    return canonical
+
+
+def _checkout_collision_record(
+    *,
+    origin: str,
+    origin_key: str,
+    group: list[dict[str, Any]],
+    representative: dict[str, Any],
+    canonical_project_path: str,
+) -> dict[str, Any]:
+    clone_groups: dict[str, list[dict[str, Any]]] = {}
+    for project in group:
+        clone_groups.setdefault(_checkout_clone_key(project), []).append(project)
+
+    representative_clone = _checkout_clone_key(representative)
+    declarations, unresolved_declarations = _declared_checkout_evidence(group)
+    declared_checkout_paths = sorted(
+        {item["target_checkout_path"] for item in declarations}, key=str.lower
+    )
+    representative_path = str(representative.get("path") or "")
+
+    clone_representatives = [
+        _checkout_representative(members, origin_key)
+        for members in clone_groups.values()
+    ]
+    clone_heads = {
+        str(_checkout_observation(project).get("head") or "")
+        for project in clone_representatives
+    }
+    observations_complete = all(
+        _checkout_observation(project).get("state") == "observed"
+        and _checkout_observation(project).get("git_common_dir")
+        for project in group
+    )
+    has_external_worktree = any(
+        project.get("_external_worktree") is True for project in group
+    )
+    has_topology_failure = any(
+        project.get("_worktree_enumeration_failed") is True for project in group
+    )
+    conflicting_heads = len(clone_heads) > 1 or "" in clone_heads
+
+    state = "selected"
+    reason_code = "single_clone_topology"
+    reason = "all discovered checkouts share one Git common directory"
+    if has_topology_failure:
+        state = "unknown"
+        reason_code = "worktree_enumeration_failed"
+        reason = "linked-worktree topology could not be enumerated"
+    elif has_external_worktree:
+        state = "unknown"
+        reason_code = "external_linked_worktree_unobserved"
+        reason = "one or more linked worktrees are outside the observed workspace"
+    elif not observations_complete:
+        state = "unknown"
+        reason_code = "checkout_observation_failed"
+        reason = "one or more same-origin checkouts could not be observed completely"
+    elif _checkout_observation(representative).get("bare") is True:
+        state = "unknown"
+        reason_code = "bare_representative_unusable"
+        reason = "the only authoritative checkout is a bare repository"
+    elif len(declared_checkout_paths) > 1:
+        state = "unknown"
+        reason_code = "conflicting_declared_checkout_paths"
+        reason = "canonical path declarations resolve to multiple checkouts"
+    elif declared_checkout_paths and representative_path not in declared_checkout_paths:
+        state = "unknown"
+        reason_code = "declared_path_conflicts_with_representative"
+        reason = (
+            "canonical path declarations resolve to a different checkout than "
+            "the compatibility representative"
+        )
+    elif unresolved_declarations:
+        state = "unknown"
+        reason_code = "declared_checkout_path_unresolved"
+        reason = "one or more canonical path declarations do not resolve to a checkout"
+    elif len(clone_groups) > 1:
+        if conflicting_heads:
+            state = "unknown"
+            reason_code = "conflicting_full_clone_heads"
+            reason = (
+                "independent same-origin clones have different or unavailable heads"
+            )
+        elif any(
+            _checkout_observation(project).get("dirty") is True
+            for project in group
+        ):
+            state = "unknown"
+            reason_code = "full_clone_local_work_present"
+            reason = "an independent same-origin clone contains local work"
+        else:
+            reason_code = "equivalent_full_clones"
+            reason = (
+                "independent same-origin clones have equivalent observed heads; "
+                "the deterministic compatibility representative is selected"
+            )
+    elif any(
+        _checkout_observation(project).get("dirty") is True for project in group
+    ):
+        state = "unknown"
+        reason_code = "linked_worktree_local_work_present"
+        reason = "a linked same-origin worktree contains local work"
+
+    checkouts = [
+        _published_checkout(
+            project,
+            representative=representative,
+            representative_clone=representative_clone,
+        )
+        for project in sorted(group, key=lambda item: str(item.get("path", "")).lower())
+    ]
+    discarded = [
+        checkout for checkout in checkouts if checkout["path"] != representative_path
+    ]
+    return {
+        "schema_version": CHECKOUT_COLLISION_SCHEMA_VERSION,
+        "origin": origin,
+        "canonical_project_path": canonical_project_path,
+        "checkout_count": len(group),
+        "full_clone_count": len(clone_groups),
+        "declared_checkout_paths": declared_checkout_paths,
+        "declared_path_evidence": declarations,
+        "unresolved_declared_paths": unresolved_declarations,
+        "selection": {
+            "state": state,
+            "reason_code": reason_code,
+            "reason": reason,
+            "representative_path": representative_path,
+            "selected_path": representative_path if state == "selected" else None,
+            "rationale": (
+                "Compatibility representative prefers a fully observed non-bare "
+                "checkout, then an origin-basename match, followed by the shallowest, "
+                "shortest, alphabetic workspace-relative path."
+            ),
+        },
+        "checkouts": checkouts,
+        "discarded_checkouts": discarded,
+    }
+
+
+def _checkout_clone_key(project: dict[str, Any]) -> str:
+    observation = _checkout_observation(project)
+    common_dir = str(observation.get("git_common_dir") or "")
+    if common_dir and (
+        observation.get("state") == "observed"
+        or project.get("_external_worktree") is True
+    ):
+        return f"observed:{common_dir}"
+    return f"unknown:{project.get('path', '')}"
+
+
+def _checkout_observation(project: dict[str, Any]) -> dict[str, Any]:
+    value = project.get("_checkout_observation")
+    if isinstance(value, dict):
+        return value
+    return {
+        "state": "unknown",
+        "head": None,
+        "branch": None,
+        "dirty": None,
+        "dirty_path_count": None,
+        "git_common_dir": None,
+        "bare": None,
+        "declared_paths": [],
+    }
+
+
+def _published_checkout(
+    project: dict[str, Any],
+    *,
+    representative: dict[str, Any],
+    representative_clone: str,
+) -> dict[str, Any]:
+    observation = _checkout_observation(project)
+    path = str(project.get("path") or "")
+    representative_path = str(representative.get("path") or "")
+    if path == representative_path:
+        relation = "representative"
+    elif _checkout_clone_key(project) == representative_clone:
+        relation = "linked_worktree"
+    else:
+        relation = "independent_full_clone"
+    return {
+        "path": path,
+        "state": str(observation.get("state") or "unknown"),
+        "relation": relation,
+        "head": observation.get("head"),
+        "branch": observation.get("branch"),
+        "dirty": observation.get("dirty"),
+        "dirty_path_count": observation.get("dirty_path_count"),
+        "bare": observation.get("bare"),
+    }
+
+
+def _declared_checkout_evidence(
+    group: list[dict[str, Any]],
+) -> tuple[list[dict[str, str]], list[str]]:
+    evidence: list[dict[str, str]] = []
+    unresolved: set[str] = set()
+    for source_project in group:
+        observation = _checkout_observation(source_project)
+        for declaration in observation.get("declared_paths") or []:
+            if declaration.get("scope") == "outside_workspace":
+                unresolved.add(str(declaration["workspace_relative_path"]))
+                continue
+            target = Path(str(declaration["absolute_path"]))
+            candidates = [
+                project
+                for project in group
+                if _path_is_within(target, Path(str(project["project_path"])))
+            ]
+            if not candidates:
+                unresolved.add(str(declaration["workspace_relative_path"]))
+                continue
+            target_project = max(
+                candidates,
+                key=lambda project: len(Path(str(project["project_path"])).parts),
+            )
+            evidence.append(
+                {
+                    "source_path": (
+                        f"{source_project['path']}/{declaration['source_file']}"
+                    ),
+                    "target_checkout_path": str(target_project["path"]),
+                }
+            )
+    unique_evidence = {
+        (item["source_path"], item["target_checkout_path"]): item for item in evidence
+    }
+    return (
+        sorted(
+            unique_evidence.values(),
+            key=lambda item: (
+                item["source_path"].lower(),
+                item["target_checkout_path"].lower(),
+            ),
+        ),
+        sorted(unresolved, key=str.lower),
+    )
+
+
 def _discover_nested_projects(
     root: Path,
     workspace_root: Path,
@@ -463,6 +921,11 @@ def _inspect_project_dir(
     context_files = _collect_context_files(project_path)
     stack = _detect_stack(project_path)
     git_facts = _gather_git_facts(project_path)
+    checkout_observation = (
+        _observe_checkout(project_path, workspace_root=workspace_root)
+        if git_facts.get("has_git")
+        else {}
+    )
     last_activity = git_facts.get("last_commit_at") or _latest_meaningful_mtime(project_path)
     context_analysis = analyze_project_context(project_path, context_files)
 
@@ -491,6 +954,7 @@ def _inspect_project_dir(
         "inferred_tool_provenance": _infer_tool_provenance(
             project_path, group_entry, context_files
         ),
+        "_checkout_observation": checkout_observation,
         "now": now,
     }
 
@@ -634,6 +1098,158 @@ def _gather_git_facts(project_path: Path) -> dict[str, Any]:
         return base
 
 
+def _observe_checkout(project_path: Path, *, workspace_root: Path) -> dict[str, Any]:
+    """Observe one discovered checkout without fetching or exposing file names."""
+    try:
+        bare = _git_read(project_path, "rev-parse", "--is-bare-repository") == "true"
+        common_dir = _git_read(
+            project_path,
+            "rev-parse",
+            "--path-format=absolute",
+            "--git-common-dir",
+        )
+        head_candidate = _git_read_optional(project_path, "rev-parse", "HEAD")
+        head = (
+            head_candidate
+            if re.fullmatch(r"[0-9a-f]{40}|[0-9a-f]{64}", head_candidate)
+            else ""
+        )
+        branch = (
+            _git_read_optional(project_path, "symbolic-ref", "--short", "HEAD")
+            if bare
+            else _git_read_optional(project_path, "branch", "--show-current")
+        )
+        if bare:
+            dirty: bool | None = None
+            dirty_path_count: int | None = None
+        else:
+            status = _git_read(
+                project_path,
+                "status",
+                "--porcelain",
+                "--untracked-files=all",
+            )
+            dirty = bool(status)
+            dirty_path_count = len(status.splitlines()) if status else 0
+    except (OSError, subprocess.CalledProcessError, subprocess.TimeoutExpired):
+        return {
+            "state": "unknown",
+            "head": None,
+            "branch": None,
+            "dirty": None,
+            "dirty_path_count": None,
+            "git_common_dir": None,
+            "bare": None,
+            "declared_paths": _declared_canonical_paths(
+                project_path, workspace_root=workspace_root
+            ),
+        }
+    return {
+        "state": "observed",
+        "head": head or None,
+        "branch": branch or None,
+        "dirty": dirty,
+        "dirty_path_count": dirty_path_count,
+        "git_common_dir": common_dir or None,
+        "bare": bare,
+        "declared_paths": _declared_canonical_paths(
+            project_path, workspace_root=workspace_root
+        ),
+    }
+
+
+def _git_read(project_path: Path, *args: str) -> str:
+    result = subprocess.run(
+        ["git", "--no-optional-locks", "-C", str(project_path), *args],
+        capture_output=True,
+        text=True,
+        timeout=5,
+        check=False,
+        env={**os.environ, "GIT_OPTIONAL_LOCKS": "0"},
+    )
+    if result.returncode != 0:
+        raise subprocess.CalledProcessError(
+            result.returncode,
+            result.args,
+            output=result.stdout,
+            stderr=result.stderr,
+        )
+    return result.stdout.strip()
+
+
+def _git_read_optional(project_path: Path, *args: str) -> str:
+    try:
+        return _git_read(project_path, *args)
+    except subprocess.CalledProcessError:
+        return ""
+
+
+def _declared_canonical_paths(
+    project_path: Path, *, workspace_root: Path
+) -> list[dict[str, str]]:
+    declarations: list[dict[str, str]] = []
+    resolved_workspace = workspace_root.resolve()
+    for source_file in ("AGENTS.md", "CLAUDE.md"):
+        path = project_path / source_file
+        try:
+            if not path.is_file() or path.stat().st_size > MAX_CONTEXT_BYTES:
+                continue
+            lines = path.read_text(errors="replace").splitlines()
+        except OSError:
+            continue
+
+        section_level: int | None = None
+        for line in lines:
+            heading = _MARKDOWN_HEADING.match(line.strip())
+            canonical_heading = _CANONICAL_PATHS_HEADING.match(line.strip())
+            if canonical_heading:
+                section_level = len(canonical_heading.group("marks"))
+                continue
+            if heading and section_level is not None:
+                if len(heading.group("marks")) <= section_level:
+                    section_level = None
+                continue
+            if section_level is None:
+                continue
+            for match in _ABSOLUTE_CODE_PATH.finditer(line):
+                candidate = Path(match.group("path")).resolve()
+                if not _path_is_within(candidate, resolved_workspace):
+                    declarations.append(
+                        {
+                            "source_file": source_file,
+                            "absolute_path": "",
+                            "workspace_relative_path": "external-checkout",
+                            "scope": "outside_workspace",
+                        }
+                    )
+                    continue
+                declarations.append(
+                    {
+                        "source_file": source_file,
+                        "absolute_path": str(candidate),
+                        "workspace_relative_path": candidate.relative_to(
+                            resolved_workspace
+                        ).as_posix(),
+                    }
+                )
+
+    unique = {
+        (item["source_file"], item["absolute_path"]): item for item in declarations
+    }
+    return sorted(
+        unique.values(),
+        key=lambda item: (item["source_file"], item["absolute_path"].lower()),
+    )
+
+
+def _path_is_within(candidate: Path, root: Path) -> bool:
+    try:
+        candidate.resolve().relative_to(root.resolve())
+        return True
+    except (OSError, ValueError):
+        return False
+
+
 def _is_bare_repository_root(project_path: Path) -> bool:
     """Recognize a conventional bare repository without climbing into parents."""
     try:
diff --git a/src/portfolio_truth_types.py b/src/portfolio_truth_types.py
index 3a2d7447..544873cb 100644
--- a/src/portfolio_truth_types.py
+++ b/src/portfolio_truth_types.py
@@ -7,10 +7,15 @@
 from typing import Any
 
 SCHEMA_VERSION = "0.11.0"
+CHECKOUT_COLLISION_SCHEMA_VERSION = "CheckoutCollisionV1"
+CHECKOUT_COLLISION_SUMMARY_SCHEMA_VERSION = "CheckoutCollisionSummaryV1"
 # 0.11.0: provenance-bearing GitHub security receipts preserve per-provider
 # states and expose complete/partial/stale/unknown coverage denominators.
 # Additive 0.11.0 fields bind normalized provider reason codes, completed-zero
 # observations, and live remote default-branch/head evidence to the same receipt.
+# Workspace discovery v3 adds versioned CheckoutCollisionV1 evidence under the
+# generic source_summary and repository_state extension points; PCC 0.11 readers
+# continue to ignore those additive keys.
 # 0.10.0: canonical producer receipts bind the exact checkout; coverage and
 # repository/worktree observation envelopes fail closed on unavailable evidence.
 # 0.8.0: derived.registry_status removed (was a stale->parked synonym table over
@@ -460,7 +465,7 @@ class PortfolioTruthSnapshot:
     coverage: list[dict[str, Any]] = field(default_factory=list)
     exclusions: dict[str, Any] = field(
         default_factory=lambda: {
-            "policy_version": "workspace_discovery.v2",
+            "policy_version": "workspace_discovery.v3",
             "counts": {},
         }
     )
diff --git a/src/portfolio_truth_validate.py b/src/portfolio_truth_validate.py
index 779ab915..061dc46a 100644
--- a/src/portfolio_truth_validate.py
+++ b/src/portfolio_truth_validate.py
@@ -20,6 +20,7 @@
     _validate_remote_repository,
     validate_normalized_security_provider,
 )
+from src.portfolio_checkout_authority import validate_checkout_authority_envelope
 from src.portfolio_pathing import (
     VALID_MATURITY_PROGRAMS,
     VALID_OPERATING_PATHS,
@@ -44,6 +45,7 @@
 from src.portfolio_truth_render import registry_project_labels
 from src.portfolio_truth_sources import WORKSPACE_EXCLUSION_REASONS
 from src.portfolio_truth_types import (
+    CHECKOUT_COLLISION_SUMMARY_SCHEMA_VERSION,
     DERIVATION_POLICY_VERSION,
     SCHEMA_VERSION,
     VALID_ACTIVITY_STATUS,
@@ -83,6 +85,7 @@ def validate_truth_snapshot(
             f"{snapshot.derivation_policy_version}"
         )
     _validate_contract_envelope(snapshot.to_dict())
+    _validate_checkout_collisions(snapshot)
     expected_order = sorted(
         snapshot.projects,
         key=lambda project: (
@@ -290,6 +293,102 @@ def validate_truth_snapshot(
         raise ValueError("PortfolioTruth coverage differs from the producer envelope.")
 
 
+def _validate_checkout_collisions(snapshot: PortfolioTruthSnapshot) -> None:
+    summary = snapshot.source_summary.get("checkout_collisions")
+    if not isinstance(summary, dict):
+        raise ValueError("Portfolio truth checkout collision summary is required.")
+    required_summary = {
+        "schema_version",
+        "state",
+        "group_count",
+        "full_clone_group_count",
+        "ambiguous_group_count",
+        "discarded_checkout_count",
+        "groups",
+    }
+    missing = sorted(required_summary - summary.keys())
+    if missing:
+        raise ValueError(f"Checkout collision summary is missing fields: {missing}")
+    if summary.get("schema_version") != CHECKOUT_COLLISION_SUMMARY_SCHEMA_VERSION:
+        raise ValueError("Unexpected checkout collision summary schema version.")
+    groups = summary.get("groups")
+    if not isinstance(groups, list):
+        raise ValueError("Checkout collision groups must be a list.")
+    _require_nonnegative_count(summary, "group_count")
+    _require_nonnegative_count(summary, "full_clone_group_count")
+    _require_nonnegative_count(summary, "ambiguous_group_count")
+    _require_nonnegative_count(summary, "discarded_checkout_count")
+    if summary["group_count"] != len(groups):
+        raise ValueError("Checkout collision group_count does not match groups.")
+
+    project_by_origin = {}
+    for project in snapshot.projects:
+        origin_key = project.identity.repo_full_name.lower()
+        if not origin_key:
+            continue
+        if origin_key in project_by_origin:
+            raise ValueError(
+                "Portfolio truth must contain one canonical project per origin: "
+                f"{project.identity.repo_full_name}"
+            )
+        project_by_origin[origin_key] = project
+    seen_origins: set[str] = set()
+    ambiguous = 0
+    full_clone_groups = 0
+    discarded_count = 0
+    for group in groups:
+        if not isinstance(group, dict):
+            raise ValueError("Checkout collision group must be an object.")
+        origin = group.get("origin")
+        if not isinstance(origin, str) or not origin.strip():
+            raise ValueError("Checkout collision origin must be non-empty.")
+        origin_key = origin.lower()
+        project = project_by_origin.get(origin_key)
+        if project is None:
+            raise ValueError(f"Checkout collision has no canonical project: {origin}")
+        validated = validate_checkout_authority_envelope(
+            group,
+            identity_path=project.identity.path,
+            repo_full_name=project.identity.repo_full_name,
+        )
+        if origin_key in seen_origins:
+            raise ValueError(f"Duplicate checkout collision origin: {origin}")
+        seen_origins.add(origin_key)
+        full_clone_groups += int(validated.full_clone_count > 1)
+        ambiguous += int(validated.state == "unknown")
+        discarded_count += validated.discarded_count
+        if project.repository_state.get("checkout_authority") != group:
+            raise ValueError(
+                "Project checkout authority differs from collision summary."
+            )
+
+    if summary["full_clone_group_count"] != full_clone_groups:
+        raise ValueError("Checkout full_clone_group_count does not match groups.")
+    if summary["ambiguous_group_count"] != ambiguous:
+        raise ValueError("Checkout ambiguous_group_count does not match groups.")
+    if summary["discarded_checkout_count"] != discarded_count:
+        raise ValueError("Checkout discarded_checkout_count does not match groups.")
+    for project in snapshot.projects:
+        authority = project.repository_state.get("checkout_authority")
+        origin_key = project.identity.repo_full_name.lower()
+        if authority is not None and origin_key not in seen_origins:
+            raise ValueError(
+                "Project checkout authority is missing from the collision summary."
+            )
+    expected_state = "unknown" if ambiguous else "observed"
+    if summary.get("state") != expected_state:
+        raise ValueError(
+            "Checkout collision summary state does not match group authority."
+        )
+
+
+def _require_nonnegative_count(value: dict, key: str) -> int:
+    count = value.get(key)
+    if isinstance(count, bool) or not isinstance(count, int) or count < 0:
+        raise ValueError(f"{key} must be a non-negative integer.")
+    return count
+
+
 def _validate_runtime_dataclass(value: object, path: str) -> None:
     """Recursively enforce postponed dataclass annotations at runtime."""
     hints = get_type_hints(type(value))
@@ -423,6 +522,7 @@ def _validate_snapshot_metadata(
         legacy_registry_rows=legacy_registry_rows,
         notion_context_rows=notion_context_rows,
         notion_context_carried_forward=notion_context_carried_forward,
+        checkout_collisions=summary["checkout_collisions"]["groups"],
     )
     if summary != expected_summary:
         raise ValueError("PortfolioTruth source summary differs from producer facts.")
@@ -430,6 +530,7 @@ def _validate_snapshot_metadata(
         catalog_errors=catalog_errors,
         catalog_warnings=catalog_warnings,
         unresolved_duplicates=summary["unresolved_duplicate_display_names"],
+        checkout_collisions=summary["checkout_collisions"]["groups"],
     )
     if snapshot.warnings != expected_warnings:
         raise ValueError("PortfolioTruth warnings differ from producer facts.")
@@ -1013,6 +1114,9 @@ def _validate_repository_state_shape(
     project_key: str,
     generated_at: datetime,
 ) -> None:
+    checkout_authority_key = (
+        {"checkout_authority"} if "checkout_authority" in repository_state else set()
+    )
     state = repository_state.get("state")
     if state not in {"observed", "unknown", "not_a_repository"}:
         raise ValueError(f"Invalid repository state for {project_key}.")
@@ -1027,7 +1131,8 @@ def _validate_repository_state_shape(
     if state == "not_a_repository":
         _require_repository_keys(
             repository_state,
-            {"state", "observed_at", "remote_default_branch"},
+            {"state", "observed_at", "remote_default_branch"}
+            | checkout_authority_key,
             project_key,
             "repository state",
         )
@@ -1041,7 +1146,8 @@ def _validate_repository_state_shape(
                 "reason_code",
                 "reason",
                 "remote_default_branch",
-            },
+            }
+            | checkout_authority_key,
             project_key,
             "repository state",
         )
@@ -1072,6 +1178,7 @@ def _validate_repository_state_shape(
                     f"Unknown repository state for {project_key} must omit null local."
                 )
             required.add("local")
+    required.update(checkout_authority_key)
     _require_repository_keys(
         repository_state,
         required,
@@ -1119,10 +1226,6 @@ def _validate_repository_state_shape(
     expected_linked_count = len(worktrees) - coordinator_count
     if kind == "working_repository":
         expected_linked_count -= 1
-        if coordinator_count:
-            raise ValueError(
-                f"Working repository topology for {project_key} has a coordinator."
-            )
     elif coordinator_count != 1:
         raise ValueError(
             f"Bare repository topology for {project_key} requires one coordinator."
@@ -1387,19 +1490,33 @@ def _validate_worktree(value: Any, *, project_key: str, index: int) -> None:
             project_key,
             label,
         )
+        observation_failed = (
+            value.get("reason_code") == "worktree_observation_failed"
+            and value.get("reason") == "git could not observe the linked worktree"
+            and _nonempty_text(value.get("path"))
+            and _optional_git_head(value.get("head"))
+            and _optional_git_branch(value.get("branch"))
+            and isinstance(value.get("detached"), bool)
+            and value.get("bare") is False
+        )
+        external_opaque = (
+            value.get("reason_code") == "external_worktree_outside_workspace"
+            and value.get("reason")
+            == "the linked worktree is outside the observed workspace"
+            and isinstance(value.get("path"), str)
+            and value["path"].startswith("external-worktree")
+            and value.get("head") is None
+            and value.get("branch") is None
+            and value.get("detached") is False
+            and isinstance(value.get("bare"), bool)
+        )
         if (
-            value.get("reason_code") != "worktree_observation_failed"
-            or value.get("reason") != "git could not observe the linked worktree"
-            or not _nonempty_text(value.get("path"))
-            or not _optional_git_head(value.get("head"))
-            or not _optional_git_branch(value.get("branch"))
-            or not isinstance(value.get("detached"), bool)
-            or value.get("bare") is not False
+            not (observation_failed or external_opaque)
             or value.get("dirty") is not None
             or value.get("dirty_path_count") is not None
         ):
             raise ValueError(f"Repository {label} for {project_key} is invalid.")
-        if (value["branch"] is None) is not value["detached"]:
+        if observation_failed and (value["branch"] is None) is not value["detached"]:
             raise ValueError(
                 f"Repository {label} branch state for {project_key} is invalid."
             )
@@ -1976,6 +2093,7 @@ def validate_portfolio_report_markdown(markdown: str) -> None:
         "# Portfolio Audit Report",
         "canonical machine-readable artifact",
         "derived from the portfolio truth snapshot",
+        "## Checkout Authority",
         "## Audit Methodology",
         "## Canonical Portfolio Truth Table",
         "## Coverage Summary",
diff --git a/src/run_instructions_audit.py b/src/run_instructions_audit.py
index c38ce914..4384b957 100644
--- a/src/run_instructions_audit.py
+++ b/src/run_instructions_audit.py
@@ -14,6 +14,10 @@
 from datetime import datetime
 from pathlib import Path
 
+from src.portfolio_checkout_authority import (
+    checkout_authority_blocker,
+    checkout_authority_path,
+)
 from src.portfolio_context_contract import (
     analyze_project_context,
     choose_primary_context_file,
@@ -86,7 +90,7 @@ def select_pilot(
 
 
 def build_record(project: dict, workspace_root: str) -> dict:
-    path = project["identity"]["path"]
+    path = checkout_authority_path(project)
     derived = project["derived"]
     context_files = derived["context_files"]
     return {
@@ -137,8 +141,24 @@ def prepare_pilot(
     generated_at = snapshot["generated_at"]
     records: list[dict] = []
     errors: list[dict] = []
+    authority_blocked = False
     for project in select_pilot(snapshot["projects"], per_tier=per_tier):
         record = build_record(project, workspace_root)
+        authority_reason = checkout_authority_blocker(
+            project,
+            workspace_root=Path(workspace_root),
+        )
+        if authority_reason:
+            authority_blocked = True
+            errors.append(
+                {
+                    "project_key": record["project_key"],
+                    "abs_path": record["abs_path"],
+                    "error": "checkout_authority_blocked",
+                    "reason": authority_reason,
+                }
+            )
+            continue
         if not Path(record["abs_path"]).is_dir():
             errors.append(
                 {
@@ -152,9 +172,10 @@ def prepare_pilot(
         record["drifted"] = compute_drifted(record["abs_path"], generated_at)
         records.append(record)
     return {
+        "state": "blocked" if authority_blocked else "ready",
         "generated_at": generated_at,
         "workspace_root": workspace_root,
-        "records": records,
+        "records": [] if authority_blocked else records,
         "errors": errors,
     }
 
@@ -165,7 +186,10 @@ def main() -> None:
     snapshot_path = (
         sys.argv[1] if len(sys.argv) > 1 else "output/portfolio-truth-latest.json"
     )
-    print(json.dumps(prepare_pilot(snapshot_path), indent=2))
+    result = prepare_pilot(snapshot_path)
+    print(json.dumps(result, indent=2))
+    if result["state"] == "blocked":
+        raise SystemExit(2)
 
 
 if __name__ == "__main__":
diff --git a/tests/test_automation_workflow.py b/tests/test_automation_workflow.py
index 8da8f50d..c2f1bee6 100644
--- a/tests/test_automation_workflow.py
+++ b/tests/test_automation_workflow.py
@@ -13,9 +13,12 @@
 
 from __future__ import annotations
 
+from copy import deepcopy
 from pathlib import Path
 
-from src.automation_executor import CommandResult
+import pytest
+
+from src.automation_executor import AutomationExecutionError, CommandResult
 from src.automation_proposals import (
     ACTION_CATALOG_SEED,
     ACTION_CONTEXT_PR,
@@ -70,6 +73,7 @@ def _project(
     has_git: bool = True,
     primary_context_file: str = "AGENTS.md",
     default_branch: str = "",
+    repository_state: dict | None = None,
 ) -> PortfolioTruthProject:
     return PortfolioTruthProject(
         identity=IdentityFields(
@@ -93,9 +97,67 @@ def _project(
             archived=False,
             path_confidence="high",
         ),
+        repository_state=repository_state or {},
     )
 
 
+def _checkout_authority(
+    *,
+    canonical_path: str = "MyRepo",
+    representative_path: str = "MyRepo",
+    origin: str = "owner/MyRepo",
+    state: str = "selected",
+    reason_code: str = "single_clone_topology",
+) -> dict:
+    other_path = (
+        f"{canonical_path}-linked"
+        if representative_path == canonical_path
+        else canonical_path
+    )
+    representative = {
+        "path": representative_path,
+        "state": "observed",
+        "relation": "representative",
+        "head": "1" * 40,
+        "branch": "main",
+        "dirty": False,
+        "dirty_path_count": 0,
+        "bare": False,
+    }
+    other = {
+        "path": other_path if state == "selected" else f"Archive/{canonical_path}",
+        "state": "observed",
+        "relation": (
+            "linked_worktree" if state == "selected" else "independent_full_clone"
+        ),
+        "head": ("1" if state == "selected" else "2") * 40,
+        "branch": "feature",
+        "dirty": False,
+        "dirty_path_count": 0,
+        "bare": False,
+    }
+    return {
+        "schema_version": "CheckoutCollisionV1",
+        "origin": origin,
+        "canonical_project_path": canonical_path,
+        "checkout_count": 2,
+        "full_clone_count": 1 if state == "selected" else 2,
+        "declared_checkout_paths": [],
+        "declared_path_evidence": [],
+        "unresolved_declared_paths": [],
+        "selection": {
+            "state": state,
+            "reason_code": reason_code,
+            "reason": "fixture authority",
+            "representative_path": representative_path,
+            "selected_path": representative_path if state == "selected" else None,
+            "rationale": "fixture selection",
+        },
+        "checkouts": [representative, other],
+        "discarded_checkouts": [other],
+    }
+
+
 def _snapshot(*projects: PortfolioTruthProject) -> PortfolioTruthSnapshot:
     from datetime import datetime, timezone
 
@@ -178,6 +240,111 @@ def test_context_pr_plan_explicit_branch_overrides_repo_default() -> None:
     assert plan.default_branch == "trunk"
 
 
+def test_context_pr_plan_blocks_unknown_checkout_authority() -> None:
+    project = _project(
+        repository_state={
+            "checkout_authority": _checkout_authority(
+                state="unknown",
+                reason_code="conflicting_full_clone_heads",
+            )
+        }
+    )
+
+    with pytest.raises(
+        AutomationExecutionError,
+        match="checkout-authority-unknown:conflicting_full_clone_heads",
+    ):
+        build_context_pr_plan(project, workspace_root=Path("/ws"))
+
+
+def test_context_pr_plan_treats_selected_path_mismatch_as_malformed() -> None:
+    project = _project(
+        repository_state={
+            "checkout_authority": _checkout_authority(
+                canonical_path="Archive/MyRepo",
+                representative_path="Archive/MyRepo",
+                reason_code="equivalent_full_clones",
+            )
+        }
+    )
+
+    with pytest.raises(
+        AutomationExecutionError,
+        match="checkout-authority-malformed",
+    ):
+        build_context_pr_plan(project, workspace_root=Path("/ws"))
+
+
+def test_context_pr_plan_uses_selected_checkout_without_replacing_identity() -> None:
+    project = _project(
+        display_name="Repo",
+        path="Repo",
+        repo_full_name="owner/Repo",
+        repository_state={
+            "checkout_authority": _checkout_authority(
+                canonical_path="Repo",
+                representative_path="_codex-worktrees/repo-main",
+                origin="owner/Repo",
+            )
+        },
+    )
+
+    plan = build_context_pr_plan(project, workspace_root=Path("/ws"))
+
+    assert project.identity.display_name == "Repo"
+    assert project.identity.path == "Repo"
+    assert plan.repo_path == Path("/ws/_codex-worktrees/repo-main")
+
+
+def test_context_pr_plan_rejects_malformed_authority_variants() -> None:
+    variants = []
+
+    missing_field = _checkout_authority()
+    missing_field.pop("origin")
+    variants.append(missing_field)
+
+    invalid_type = _checkout_authority()
+    invalid_type["selection"] = "selected"
+    variants.append(invalid_type)
+
+    invalid_count = _checkout_authority()
+    invalid_count["checkout_count"] = 3
+    variants.append(invalid_count)
+
+    malformed_record = _checkout_authority()
+    del malformed_record["checkouts"][0]["head"]
+    variants.append(malformed_record)
+
+    unknown_discarded = _checkout_authority()
+    unknown_discarded["checkouts"][1].update(
+        {
+            "state": "unknown",
+            "head": None,
+            "branch": None,
+            "dirty": None,
+            "dirty_path_count": None,
+            "bare": None,
+        }
+    )
+    variants.append(unknown_discarded)
+
+    dirty_discarded = _checkout_authority()
+    dirty_discarded["checkouts"][1].update(
+        {"dirty": True, "dirty_path_count": 1}
+    )
+    variants.append(dirty_discarded)
+
+    for authority in variants:
+        project = _project(
+            repository_state={"checkout_authority": deepcopy(authority)}
+        )
+        with pytest.raises(
+            AutomationExecutionError,
+            match="checkout-authority-malformed",
+        ):
+            build_context_pr_plan(project, workspace_root=Path("/ws"))
+
+
 def test_context_pr_plan_apply_change_writes_managed_block(tmp_path: Path) -> None:
     project = _project(path="MyRepo")
     repo_path = tmp_path / "MyRepo"
@@ -335,6 +502,36 @@ def test_execute_catalog_seed_applies_and_persists_executed(tmp_path: Path) -> N
     assert persisted.execution_ref == str(catalog_path)
 
 
+def test_execute_catalog_seed_blocks_unknown_checkout_authority(tmp_path: Path) -> None:
+    proposals_path = tmp_path / "pending-proposals.json"
+    _write(proposals_path, _proposal(action_type=ACTION_CATALOG_SEED))
+    catalog_path = tmp_path / "catalog.yaml"
+    project = _project(
+        repository_state={
+            "checkout_authority": _checkout_authority(
+                state="unknown",
+                reason_code="conflicting_full_clone_heads",
+            )
+        }
+    )
+
+    results = execute_approved_proposals(
+        proposals_path=proposals_path,
+        snapshot=_snapshot(project),
+        workspace_root=tmp_path,
+        catalog_path=catalog_path,
+        executed_at=NOW,
+        dry_run=False,
+    )
+
+    assert results[0].outcome == "failed"
+    assert results[0].detail == (
+        "checkout-authority-unknown:conflicting_full_clone_heads"
+    )
+    assert not catalog_path.exists()
+    assert load_proposals(proposals_path)[0].status == STATUS_APPROVED
+
+
 # --- execute_approved_proposals: resolution + slug policy ------------------
 
 
diff --git a/tests/test_demo_portfolio.py b/tests/test_demo_portfolio.py
index cc18f992..fa049586 100644
--- a/tests/test_demo_portfolio.py
+++ b/tests/test_demo_portfolio.py
@@ -33,6 +33,10 @@
     _provider_result,
 )
 from src.portfolio_pathing import build_operating_path_entry
+from src.portfolio_truth_sources import (
+    WORKSPACE_DISCOVERY_POLICY_VERSION,
+    checkout_collision_summary,
+)
 from src.portfolio_truth_provenance import REQUIRED_PROJECT_PROVENANCE_KEYS
 from src.portfolio_truth_types import (
     SCHEMA_VERSION,
@@ -98,9 +102,12 @@ def test_schema_version_tracks_the_producer_constant() -> None:
 def test_envelope_collection_shapes_match_the_canonical_serializer() -> None:
     snapshot = _snapshot()
 
+    assert snapshot["source_summary"]["checkout_collisions"] == (
+        checkout_collision_summary([])
+    )
     assert snapshot["inputs"] == _expected_inputs(snapshot)
     assert snapshot["exclusions"] == {
-        "policy_version": "workspace_discovery.v2",
+        "policy_version": WORKSPACE_DISCOVERY_POLICY_VERSION,
         "counts": {},
     }
     assert snapshot["producer"] == {}
@@ -121,7 +128,7 @@ def test_committed_demo_truth_artifacts_match_the_canonical_envelope() -> None:
         snapshot = json.loads(path.read_text())
         assert snapshot["inputs"] == _expected_inputs(snapshot)
         assert snapshot["exclusions"] == {
-            "policy_version": "workspace_discovery.v2",
+            "policy_version": WORKSPACE_DISCOVERY_POLICY_VERSION,
             "counts": {},
         }
         assert snapshot["producer"] == {}
diff --git a/tests/test_operator_os_seam_linter.py b/tests/test_operator_os_seam_linter.py
index ac65932d..99a955e7 100644
--- a/tests/test_operator_os_seam_linter.py
+++ b/tests/test_operator_os_seam_linter.py
@@ -326,7 +326,7 @@ def test_contract_shadow_fails_when_excluded_backup_leaks_into_projects(
             "source_summary": {"attention_state_counts": {"decision-needed": 1}},
             "rollups": {"decision": {"decision_needed_count": 1}},
             "exclusions": {
-                "policy_version": "workspace_discovery.v2",
+                "policy_version": "workspace_discovery.v3",
                 "counts": {},
             },
             "projects": [
diff --git a/tests/test_portfolio_automation.py b/tests/test_portfolio_automation.py
index 2919338a..7725f91c 100644
--- a/tests/test_portfolio_automation.py
+++ b/tests/test_portfolio_automation.py
@@ -8,6 +8,8 @@
 
 from __future__ import annotations
 
+from copy import deepcopy
+
 from src.portfolio_automation import (
     AutomationCandidate,
     AutomationEligibility,
@@ -27,9 +29,14 @@ def _project(
     activity_status: str = "active",
     path_confidence: str = "high",
     context_quality: str = "standard",
+    checkout_authority: dict | None = None,
 ) -> dict:
-    return {
-        "identity": {"display_name": display_name, "repo_full_name": repo_full_name},
+    project = {
+        "identity": {
+            "display_name": display_name,
+            "repo_full_name": repo_full_name,
+            "path": display_name,
+        },
         "declared": {"operating_path": "maintain"},
         "derived": {
             "activity_status": activity_status,
@@ -37,6 +44,54 @@ def _project(
             "context_quality": context_quality,
         },
     }
+    if checkout_authority is not None:
+        project["repository_state"] = {"checkout_authority": checkout_authority}
+    return project
+
+
+def _authority(*, state: str = "selected", reason_code: str = "single_clone_topology") -> dict:
+    representative = {
+        "path": "Repo",
+        "state": "observed",
+        "relation": "representative",
+        "head": "1" * 40,
+        "branch": "main",
+        "dirty": False,
+        "dirty_path_count": 0,
+        "bare": False,
+    }
+    other = {
+        "path": "Repo-linked" if state == "selected" else "Archive/Repo",
+        "state": "observed",
+        "relation": (
+            "linked_worktree" if state == "selected" else "independent_full_clone"
+        ),
+        "head": ("1" if state == "selected" else "2") * 40,
+        "branch": "feature",
+        "dirty": False,
+        "dirty_path_count": 0,
+        "bare": False,
+    }
+    return {
+        "schema_version": "CheckoutCollisionV1",
+        "origin": "owner/Repo",
+        "canonical_project_path": "Repo",
+        "checkout_count": 2,
+        "full_clone_count": 1 if state == "selected" else 2,
+        "declared_checkout_paths": [],
+        "declared_path_evidence": [],
+        "unresolved_declared_paths": [],
+        "selection": {
+            "state": state,
+            "reason_code": reason_code,
+            "reason": "fixture authority",
+            "representative_path": "Repo",
+            "selected_path": "Repo" if state == "selected" else None,
+            "rationale": "fixture selection",
+        },
+        "checkouts": [representative, other],
+        "discarded_checkouts": [other],
+    }
 
 
 # --- evaluate_automation_eligibility ---------------------------------------
@@ -137,6 +192,114 @@ def test_multiple_blockers_accumulate() -> None:
     }
 
 
+def test_unknown_checkout_authority_blocks_automation_candidate() -> None:
+    result = evaluate_automation_eligibility(
+        _project(
+            checkout_authority=_authority(
+                state="unknown",
+                reason_code="conflicting_full_clone_heads",
+            )
+        ),
+        decision_quality_status="trusted",
+    )
+
+    assert result.eligible is False
+    assert result.blockers == (
+        "checkout-authority-unknown:conflicting_full_clone_heads",
+    )
+
+
+def test_observed_selected_checkout_authority_remains_eligible() -> None:
+    result = evaluate_automation_eligibility(
+        _project(checkout_authority=_authority()),
+        decision_quality_status="trusted",
+    )
+
+    assert result.eligible is True
+    assert result.blockers == ()
+
+
+def test_multiple_observed_worktrees_require_checkout_authority() -> None:
+    project = _project()
+    project["repository_state"] = {
+        "state": "observed",
+        "worktrees": [
+            {"state": "observed", "path": "/workspace/Repo", "dirty": False},
+            {
+                "state": "observed",
+                "path": "/workspace/_codex-worktrees/repo-feature",
+                "dirty": False,
+            },
+        ],
+    }
+
+    result = evaluate_automation_eligibility(
+        project,
+        decision_quality_status="trusted",
+    )
+
+    assert result.eligible is False
+    assert result.blockers == ("checkout-authority-missing:multiple-worktrees",)
+
+
+def test_checkout_authority_must_cover_repository_worktree_topology() -> None:
+    project = _project(checkout_authority=_authority())
+    project["repository_state"].update(
+        {
+            "state": "observed",
+            "worktrees": [
+                {"state": "observed", "path": "/workspace/Repo", "dirty": False},
+                {
+                    "state": "observed",
+                    "path": "/outside/repo-feature",
+                    "dirty": False,
+                },
+                {
+                    "state": "observed",
+                    "path": "/outside/repo-review",
+                    "dirty": False,
+                },
+            ],
+        }
+    )
+
+    result = evaluate_automation_eligibility(
+        project,
+        decision_quality_status="trusted",
+    )
+
+    assert result.eligible is False
+    assert result.blockers == ("checkout-authority-topology-mismatch",)
+
+
+def test_malformed_checkout_authority_variants_block_automation() -> None:
+    variants = []
+
+    missing_field = _authority()
+    missing_field.pop("origin")
+    variants.append(missing_field)
+
+    invalid_type = _authority()
+    invalid_type["selection"] = "selected"
+    variants.append(invalid_type)
+
+    invalid_count = _authority()
+    invalid_count["checkout_count"] = 3
+    variants.append(invalid_count)
+
+    malformed_record = _authority()
+    del malformed_record["checkouts"][0]["head"]
+    variants.append(malformed_record)
+
+    for authority in variants:
+        result = evaluate_automation_eligibility(
+            _project(checkout_authority=deepcopy(authority)),
+            decision_quality_status="trusted",
+        )
+        assert result.eligible is False
+        assert result.blockers == ("checkout-authority-malformed",)
+
+
 # --- select_automation_candidates ------------------------------------------
 
 
diff --git a/tests/test_portfolio_repository_state.py b/tests/test_portfolio_repository_state.py
index 3e8a3b5f..543c1a75 100644
--- a/tests/test_portfolio_repository_state.py
+++ b/tests/test_portfolio_repository_state.py
@@ -8,6 +8,7 @@
 
 import pytest
 
+import src.portfolio_repository_state as repository_state
 from src.portfolio_repository_state import (
     _local_from_worktree,
     _observed_result,
@@ -67,7 +68,7 @@ def test_observation_reports_dirty_no_upstream_and_unknown_remote(
     repo = _repo(tmp_path)
     (repo / "dirty.txt").write_text("dirty\n")
 
-    state = observe_repository_state(
+    state = repository_state.observe_repository_state(
         repo, observed_at=datetime(2026, 7, 12, tzinfo=UTC)
     )
 
@@ -334,7 +335,7 @@ def test_bare_coordinator_selects_unique_clean_remote_default_worktree(
     linked = tmp_path / "linked"
     _git(bare, "worktree", "add", str(linked), "main")
 
-    state = observe_repository_state(
+    state = repository_state.observe_repository_state(
         bare,
         observed_at=datetime(2026, 7, 12, tzinfo=UTC),
         remote_default_branch=_remote_default(head),
@@ -357,7 +358,7 @@ def test_multiple_remote_head_candidates_use_default_branch_tiebreak(
     detached = tmp_path / "detached"
     _git(repo, "worktree", "add", "--detach", str(detached), head)
 
-    state = observe_repository_state(
+    state = repository_state.observe_repository_state(
         repo,
         observed_at=datetime(2026, 7, 12, tzinfo=UTC),
         remote_default_branch=_remote_default(head),
@@ -391,7 +392,7 @@ def test_recovery_tracking_does_not_impersonate_remote_default(
     )
     _git(repo, "branch", "--set-upstream-to=origin/recovery/repo-main", "main")
 
-    state = observe_repository_state(
+    state = repository_state.observe_repository_state(
         repo,
         observed_at=datetime(2026, 7, 12, tzinfo=UTC),
         remote_default_branch=_remote_default(remote_head),
@@ -413,7 +414,7 @@ def test_bare_coordinator_missing_remote_evidence_is_precise_unknown(
     linked = tmp_path / "linked"
     _git(bare, "worktree", "add", str(linked), "main")
 
-    state = observe_repository_state(
+    state = repository_state.observe_repository_state(
         bare,
         observed_at=datetime(2026, 7, 12, tzinfo=UTC),
     )
@@ -515,7 +516,7 @@ def test_ambiguous_remote_default_worktrees_fail_closed(tmp_path: Path) -> None:
     _git(bare, "worktree", "add", "--detach", str(first), head)
     _git(bare, "worktree", "add", "--detach", str(second), head)
 
-    state = observe_repository_state(
+    state = repository_state.observe_repository_state(
         bare,
         observed_at=datetime(2026, 7, 12, tzinfo=UTC),
         remote_default_branch=_remote_default(head),
diff --git a/tests/test_portfolio_truth.py b/tests/test_portfolio_truth.py
index bd247f01..a744d5a6 100644
--- a/tests/test_portfolio_truth.py
+++ b/tests/test_portfolio_truth.py
@@ -6,6 +6,8 @@
 import subprocess
 import threading
 import time
+from copy import deepcopy
+from dataclasses import replace
 from datetime import datetime, timedelta, timezone
 from pathlib import Path
 
@@ -27,6 +29,11 @@
     apply_context_recovery_plan,
     build_context_recovery_plan,
 )
+from src.portfolio_checkout_authority import (
+    checkout_authority_blocker,
+    checkout_authority_path,
+    validate_checkout_authority_envelope,
+)
 from src.portfolio_truth_publish import (
     PortfolioTruthPublishError,
     publish_portfolio_truth,
@@ -41,6 +48,7 @@
 from src.portfolio_truth_sources import (
     _classify_context_quality,
     _extract_github_full_name,
+    _git_read,
     _git_remote_full_name,
     load_safe_notion_project_context,
 )
@@ -60,11 +68,64 @@ def _write(path: Path, content: str) -> None:
 def _set_mtime(path: Path, timestamp: float) -> None:
     path.touch()
     path.chmod(0o644)
-    import os
-
     os.utime(path, (timestamp, timestamp))
 
 
+def _checkout_authority_fixture(
+    *,
+    canonical_path: str,
+    origin: str,
+    state: str = "selected",
+    reason_code: str = "single_clone_topology",
+) -> dict:
+    representative = {
+        "path": canonical_path,
+        "state": "observed",
+        "relation": "representative",
+        "head": "1" * 40,
+        "branch": "main",
+        "dirty": False,
+        "dirty_path_count": 0,
+        "bare": False,
+    }
+    other = {
+        "path": (
+            f"{canonical_path}-linked"
+            if state == "selected"
+            else f"Archive/{canonical_path}"
+        ),
+        "state": "observed",
+        "relation": (
+            "linked_worktree" if state == "selected" else "independent_full_clone"
+        ),
+        "head": ("1" if state == "selected" else "2") * 40,
+        "branch": "feature",
+        "dirty": False,
+        "dirty_path_count": 0,
+        "bare": False,
+    }
+    return {
+        "schema_version": "CheckoutCollisionV1",
+        "origin": origin,
+        "canonical_project_path": canonical_path,
+        "checkout_count": 2,
+        "full_clone_count": 1 if state == "selected" else 2,
+        "declared_checkout_paths": [],
+        "declared_path_evidence": [],
+        "unresolved_declared_paths": [],
+        "selection": {
+            "state": state,
+            "reason_code": reason_code,
+            "reason": "fixture authority",
+            "representative_path": canonical_path,
+            "selected_path": canonical_path if state == "selected" else None,
+            "rationale": "fixture selection",
+        },
+        "checkouts": [representative, other],
+        "discarded_checkouts": [other],
+    }
+
+
 def _security_test_project(
     name: str,
     *,
@@ -446,132 +507,1034 @@ def legacy_registry(tmp_path: Path) -> Path:
 
 | Project | Status | Tool | Context Quality | Stack | Context Files | Category | Notes |
 |---------|--------|------|-----------------|-------|---------------|----------|-------|
-| Alpha | parked | claude-code | standard | Next.js | CLAUDE.md | commercial | Legacy row |
-
-## ITPRJsViaClaude/ (IT Tools — 1 projects)
-
-| Project | Status | Tool | Context Quality | Context Files | Notes |
-|---------|--------|------|-----------------|---------------|-------|
-| Beta | parked | codex | boilerplate | AGENTS.md | Legacy beta |
+| Alpha | parked | claude-code | standard | Next.js | CLAUDE.md | commercial | Legacy row |
+
+## ITPRJsViaClaude/ (IT Tools — 1 projects)
+
+| Project | Status | Tool | Context Quality | Context Files | Notes |
+|---------|--------|------|-----------------|---------------|-------|
+| Beta | parked | codex | boilerplate | AGENTS.md | Legacy beta |
+"""
+    )
+    return path
+
+
+def test_truth_snapshot_respects_declared_and_derived_fields(
+    portfolio_workspace: Path,
+    portfolio_catalog: Path,
+    legacy_registry: Path,
+) -> None:
+    now = datetime.fromtimestamp(1_700_200_000, tz=timezone.utc)
+    result = build_portfolio_truth_snapshot(
+        workspace_root=portfolio_workspace,
+        catalog_path=portfolio_catalog,
+        legacy_registry_path=legacy_registry,
+        include_notion=False,
+        now=now,
+    )
+
+    projects = {
+        project.identity.display_name: project for project in result.snapshot.projects
+    }
+    alpha = projects["Alpha"]
+    beta = projects["Beta"]
+    gamma = projects["Calibrate"]
+
+    for project in projects.values():
+        assert REQUIRED_PROJECT_PROVENANCE_KEYS <= project.provenance.keys()
+
+    assert alpha.identity.project_key == "Alpha"
+    assert alpha.declared.owner == "d"
+    assert alpha.declared.category == "commercial"
+    assert alpha.declared.operating_path == "maintain"
+    assert alpha.derived.context_quality == "full"
+    assert alpha.derived.activity_status == "active"
+    assert alpha.derived.archived is False
+    assert alpha.derived.attention_state == "active-product"
+    assert alpha.derived.primary_context_file == "CLAUDE.md"
+    assert alpha.derived.project_summary_present is True
+    assert alpha.derived.next_recommended_move_present is True
+    assert hasattr(alpha.declared, "doctor_standard")
+    assert hasattr(alpha.declared, "automation_eligible")
+    assert alpha.declared.automation_eligible is False
+    assert hasattr(alpha, "risk")
+    assert alpha.risk.risk_tier in {"elevated", "moderate", "baseline", "deferred"}
+
+    assert beta.identity.section_marker == "ITPRJsViaClaude/"
+    assert beta.declared.category == "it-work"
+    assert beta.derived.context_quality == "boilerplate"
+    assert beta.derived.activity_status == "stale"
+    assert beta.derived.attention_state == "parked"
+
+    assert gamma.identity.section_marker == "iOS Projects"
+    assert gamma.derived.stack == ["Swift"]
+
+    assert result.snapshot.schema_version == "0.11.0"
+    assert result.snapshot.derivation_policy_version == "portfolio_attention.v3"
+    assert result.snapshot.inputs["catalog"]["sha256"]
+    assert result.snapshot.inputs["notion"]["mode"] == "unavailable"
+    assert result.snapshot.exclusions == {
+        "policy_version": "workspace_discovery.v3",
+        "counts": {},
+    }
+    assert (
+        result.snapshot.source_summary["attention_state_counts"]["active-product"] == 1
+    )
+    assert result.snapshot.source_summary["attention_state_counts"]["parked"] == 1
+    assert result.snapshot.source_summary["checkout_collisions"] == {
+        "schema_version": "CheckoutCollisionSummaryV1",
+        "state": "observed",
+        "group_count": 0,
+        "full_clone_group_count": 0,
+        "ambiguous_group_count": 0,
+        "discarded_checkout_count": 0,
+        "groups": [],
+    }
+
+    # Derived rollups are emitted so downstream consumers (command-center) read
+    # them instead of re-deriving the auditor's risk/security logic.
+    snapshot_dict = result.snapshot.to_dict()
+    rollups = snapshot_dict["rollups"]
+    assert set(rollups["risk_tier_counts"]) == {
+        "elevated",
+        "moderate",
+        "baseline",
+        "deferred",
+    }
+    assert sum(rollups["risk_tier_counts"].values()) == len(result.snapshot.projects)
+    assert set(rollups["security"]) == {
+        "scanned_count",
+        "unavailable_count",
+        "complete_repo_count",
+        "partial_repo_count",
+        "stale_count",
+        "unknown_count",
+        "cohort_repository_count",
+        "cohort_complete_count",
+        "cohort_partial_count",
+        "cohort_stale_count",
+        "cohort_unknown_count",
+        "dependabot_observed_count",
+        "code_scanning_observed_count",
+        "secret_scanning_observed_count",
+        "dependabot_zero_finding_count",
+        "code_scanning_zero_finding_count",
+        "secret_scanning_zero_finding_count",
+        "remote_default_branch_observed_count",
+        "remote_default_branch_partial_count",
+        "remote_default_branch_stale_count",
+        "remote_default_branch_unavailable_count",
+        "coverage_state",
+        "repos_with_open_high_critical",
+        "total_open_high",
+        "total_open_critical",
+    }
+    assert rollups["security"]["cohort_repository_count"] == 1
+    assert rollups["security"]["cohort_unknown_count"] == 1
+    assert rollups["security"]["cohort_complete_count"] == 0
+    assert set(rollups["decision"]) == {
+        "decision_needed_count",
+        "default_attention_count",
+    }
+    assert (
+        rollups["decision"]["default_attention_count"]
+        >= rollups["decision"]["decision_needed_count"]
+    )
+    # Per-project open_high_critical is emitted in the security block.
+    assert "open_high_critical" in snapshot_dict["projects"][0]["security"]
+
+
+def test_checkout_collision_flows_through_truth_validation_and_report(
+    portfolio_workspace: Path,
+    portfolio_catalog: Path,
+    legacy_registry: Path,
+) -> None:
+    root_clone = portfolio_workspace / "Widget"
+    nested_clone = portfolio_workspace / "Archive" / "Widget"
+    heads: list[str] = []
+    for index, clone in enumerate((root_clone, nested_clone), start=1):
+        clone.mkdir(parents=True)
+        _write(clone / "README.md", f"# Widget {index}\n")
+        subprocess.run(
+            ["git", "init", "-q", "-b", "main"],
+            cwd=clone,
+            check=True,
+        )
+        subprocess.run(
+            ["git", "remote", "add", "origin", "git@github.com:owner/Widget.git"],
+            cwd=clone,
+            check=True,
+        )
+        subprocess.run(["git", "add", "README.md"], cwd=clone, check=True)
+        subprocess.run(
+            [
+                "git",
+                "-c",
+                "user.name=Test",
+                "-c",
+                "user.email=test@example.invalid",
+                "commit",
+                "-q",
+                "-m",
+                f"fixture {index}",
+            ],
+            cwd=clone,
+            check=True,
+        )
+        heads.append(
+            subprocess.run(
+                ["git", "rev-parse", "HEAD"],
+                cwd=clone,
+                check=True,
+                capture_output=True,
+                text=True,
+            ).stdout.strip()
+        )
+
+    result = build_portfolio_truth_snapshot(
+        workspace_root=portfolio_workspace,
+        catalog_path=portfolio_catalog,
+        legacy_registry_path=legacy_registry,
+        include_notion=False,
+        now=datetime(2026, 8, 3, tzinfo=timezone.utc),
+    )
+
+    widget_projects = [
+        project
+        for project in result.snapshot.projects
+        if project.identity.repo_full_name == "owner/Widget"
+    ]
+    assert len(widget_projects) == 1
+    assert widget_projects[0].identity.path == "Widget"
+    summary = result.snapshot.source_summary["checkout_collisions"]
+    assert summary["group_count"] == 1
+    assert summary["ambiguous_group_count"] == 1
+    assert summary["discarded_checkout_count"] == 1
+    group = summary["groups"][0]
+    assert group["selection"]["state"] == "unknown"
+    assert group["selection"]["reason_code"] == "conflicting_full_clone_heads"
+    assert widget_projects[0].repository_state["checkout_authority"] == group
+    validate_truth_snapshot(result.snapshot)
+
+    markdown = render_portfolio_report_markdown(result.snapshot, "output/x.json")
+    assert "## Checkout Authority" in markdown
+    assert "`owner/Widget`" in markdown
+    assert "`conflicting_full_clone_heads`" in markdown
+    assert "`Archive/Widget`" in markdown
+    assert heads[1] in markdown
+    validate_portfolio_report_markdown(markdown)
+
+    duplicate_project = replace(
+        widget_projects[0],
+        identity=replace(
+            widget_projects[0].identity,
+            project_key="widget-duplicate",
+            path="Archive/Widget",
+        ),
+    )
+    duplicate_snapshot = replace(
+        result.snapshot,
+        projects=[*result.snapshot.projects, duplicate_project],
+    )
+    with pytest.raises(ValueError, match="one canonical project per origin"):
+        validate_truth_snapshot(duplicate_snapshot)
+
+    summary["discarded_checkout_count"] += 1
+    with pytest.raises(ValueError, match="discarded_checkout_count"):
+        validate_truth_snapshot(result.snapshot)
+
+
+def test_unresolved_declared_checkout_flows_through_truth_validation(
+    portfolio_workspace: Path,
+    portfolio_catalog: Path,
+    legacy_registry: Path,
+) -> None:
+    repo = portfolio_workspace / "Repo"
+    repo.mkdir()
+    missing_target = portfolio_workspace / "_codex-worktrees" / "repo-retired" / "src"
+    _write(
+        repo / "AGENTS.md",
+        "# Repo\n\n## Canonical Paths\n\n"
+        f"- Source: `{missing_target}`\n",
+    )
+    subprocess.run(["git", "init", "-q", "-b", "main"], cwd=repo, check=True)
+    subprocess.run(
+        ["git", "remote", "add", "origin", "git@github.com:owner/Repo.git"],
+        cwd=repo,
+        check=True,
+    )
+    subprocess.run(["git", "add", "AGENTS.md"], cwd=repo, check=True)
+    subprocess.run(
+        [
+            "git",
+            "-c",
+            "user.name=Test",
+            "-c",
+            "user.email=test@example.invalid",
+            "commit",
+            "-q",
+            "-m",
+            "fixture",
+        ],
+        cwd=repo,
+        check=True,
+    )
+
+    result = build_portfolio_truth_snapshot(
+        workspace_root=portfolio_workspace,
+        catalog_path=portfolio_catalog,
+        legacy_registry_path=legacy_registry,
+        include_notion=False,
+        now=datetime(2026, 8, 3, tzinfo=timezone.utc),
+    )
+
+    project = next(
+        item
+        for item in result.snapshot.projects
+        if item.identity.repo_full_name == "owner/Repo"
+    )
+    authority = project.repository_state["checkout_authority"]
+    assert authority["checkout_count"] == 1
+    assert authority["selection"]["state"] == "unknown"
+    assert (
+        authority["selection"]["reason_code"]
+        == "declared_checkout_path_unresolved"
+    )
+    assert authority["unresolved_declared_paths"] == [
+        "_codex-worktrees/repo-retired/src"
+    ]
+    validate_truth_snapshot(result.snapshot)
+
+
+def test_failed_singleton_observation_with_declaration_is_valid_unknown(
+    portfolio_workspace: Path,
+    portfolio_catalog: Path,
+    legacy_registry: Path,
+    monkeypatch,
+) -> None:
+    repo = portfolio_workspace / "ObservationRepo"
+    repo.mkdir()
+    declared_target = repo / "src"
+    _write(
+        repo / "AGENTS.md",
+        "# ObservationRepo\n\n## Canonical Paths\n\n"
+        f"- Source: `{declared_target}`\n",
+    )
+    subprocess.run(["git", "init", "-q", "-b", "main"], cwd=repo, check=True)
+    subprocess.run(
+        [
+            "git",
+            "remote",
+            "add",
+            "origin",
+            "git@github.com:owner/ObservationRepo.git",
+        ],
+        cwd=repo,
+        check=True,
+    )
+    subprocess.run(["git", "add", "AGENTS.md"], cwd=repo, check=True)
+    subprocess.run(
+        [
+            "git",
+            "-c",
+            "user.name=Test",
+            "-c",
+            "user.email=test@example.invalid",
+            "commit",
+            "-q",
+            "-m",
+            "fixture",
+        ],
+        cwd=repo,
+        check=True,
+    )
+
+    def _timeout_status(project_path: Path, *args: str) -> str:
+        if args and args[0] == "status":
+            raise subprocess.TimeoutExpired(["git", "status"], timeout=5)
+        return _git_read(project_path, *args)
+
+    monkeypatch.setattr(
+        "src.portfolio_truth_sources._git_read",
+        _timeout_status,
+    )
+
+    result = build_portfolio_truth_snapshot(
+        workspace_root=portfolio_workspace,
+        catalog_path=portfolio_catalog,
+        legacy_registry_path=legacy_registry,
+        include_notion=False,
+        now=datetime(2026, 8, 3, tzinfo=timezone.utc),
+    )
+
+    project = next(
+        item
+        for item in result.snapshot.projects
+        if item.identity.repo_full_name == "owner/ObservationRepo"
+    )
+    authority = project.repository_state["checkout_authority"]
+    assert authority["checkout_count"] == 1
+    assert authority["selection"]["state"] == "unknown"
+    assert authority["selection"]["reason_code"] == "checkout_observation_failed"
+    assert authority["selection"]["selected_path"] is None
+    assert authority["declared_checkout_paths"] == ["ObservationRepo"]
+    assert checkout_authority_blocker(
+        project,
+        workspace_root=portfolio_workspace,
+    ) == "checkout-authority-unknown:checkout_observation_failed"
+    validate_truth_snapshot(result.snapshot)
+
+
+def test_declared_bare_singleton_publishes_unknown_and_blocks_consumers(
+    portfolio_workspace: Path,
+    portfolio_catalog: Path,
+    legacy_registry: Path,
+) -> None:
+    seed = portfolio_workspace / "_backups" / "bare-seed"
+    seed.mkdir(parents=True)
+    _write(seed / "README.md", "# BareRepo\n")
+    subprocess.run(["git", "init", "-q", "-b", "main"], cwd=seed, check=True)
+    subprocess.run(["git", "add", "README.md"], cwd=seed, check=True)
+    subprocess.run(
+        [
+            "git",
+            "-c",
+            "user.name=Test",
+            "-c",
+            "user.email=test@example.invalid",
+            "commit",
+            "-q",
+            "-m",
+            "fixture",
+        ],
+        cwd=seed,
+        check=True,
+    )
+    coordinator = portfolio_workspace / "BareRepo"
+    subprocess.run(
+        ["git", "clone", "-q", "--bare", str(seed), str(coordinator)],
+        check=True,
+    )
+    subprocess.run(
+        [
+            "git",
+            "remote",
+            "set-url",
+            "origin",
+            "git@github.com:owner/BareRepo.git",
+        ],
+        cwd=coordinator,
+        check=True,
+    )
+    _write(
+        coordinator / "AGENTS.md",
+        "# BareRepo\n\n## Canonical Paths\n\n"
+        f"- Source: `{coordinator}`\n",
+    )
+
+    result = build_portfolio_truth_snapshot(
+        workspace_root=portfolio_workspace,
+        catalog_path=portfolio_catalog,
+        legacy_registry_path=legacy_registry,
+        include_notion=False,
+        now=datetime(2026, 8, 3, tzinfo=timezone.utc),
+    )
+
+    project = next(
+        item
+        for item in result.snapshot.projects
+        if item.identity.repo_full_name == "owner/BareRepo"
+    )
+    authority = project.repository_state["checkout_authority"]
+    assert authority["checkout_count"] == 1
+    assert authority["selection"]["state"] == "unknown"
+    assert authority["selection"]["selected_path"] is None
+    assert authority["selection"]["reason_code"] == "bare_representative_unusable"
+    assert checkout_authority_blocker(
+        project,
+        workspace_root=portfolio_workspace,
+    ) == "checkout-authority-unknown:bare_representative_unusable"
+    validate_truth_snapshot(result.snapshot)
+
+    plan = build_context_recovery_plan(
+        result.snapshot,
+        workspace_root=portfolio_workspace,
+    )
+    target = next(item for item in plan.projects if item.project_key == "BareRepo")
+    assert target.status == "skipped"
+    assert target.reason == "checkout-authority-unknown:bare_representative_unusable"
+
+
+def test_worktree_enumeration_failure_is_explicit_unknown_summary(
+    portfolio_workspace: Path,
+    portfolio_catalog: Path,
+    legacy_registry: Path,
+    monkeypatch,
+) -> None:
+    repo = portfolio_workspace / "TopologyRepo"
+    repo.mkdir()
+    _write(repo / "README.md", "# TopologyRepo\n")
+    subprocess.run(["git", "init", "-q", "-b", "main"], cwd=repo, check=True)
+    subprocess.run(
+        [
+            "git",
+            "remote",
+            "add",
+            "origin",
+            "git@github.com:owner/TopologyRepo.git",
+        ],
+        cwd=repo,
+        check=True,
+    )
+    subprocess.run(["git", "add", "README.md"], cwd=repo, check=True)
+    subprocess.run(
+        [
+            "git",
+            "-c",
+            "user.name=Test",
+            "-c",
+            "user.email=test@example.invalid",
+            "commit",
+            "-q",
+            "-m",
+            "fixture",
+        ],
+        cwd=repo,
+        check=True,
+    )
+
+    def _timeout_worktree_enumeration(_project_path: Path) -> list[Path]:
+        raise subprocess.TimeoutExpired(["git", "worktree", "list"], timeout=5)
+
+    monkeypatch.setattr(
+        "src.portfolio_truth_sources._git_worktree_paths",
+        _timeout_worktree_enumeration,
+    )
+
+    result = build_portfolio_truth_snapshot(
+        workspace_root=portfolio_workspace,
+        catalog_path=portfolio_catalog,
+        legacy_registry_path=legacy_registry,
+        include_notion=False,
+        now=datetime(2026, 8, 3, tzinfo=timezone.utc),
+    )
+
+    project = next(
+        item
+        for item in result.snapshot.projects
+        if item.identity.repo_full_name == "owner/TopologyRepo"
+    )
+    authority = project.repository_state["checkout_authority"]
+    assert authority["checkout_count"] == 1
+    assert authority["selection"]["state"] == "unknown"
+    assert authority["selection"]["reason_code"] == "worktree_enumeration_failed"
+    summary = result.snapshot.source_summary["checkout_collisions"]
+    assert summary["state"] == "unknown"
+    assert summary["group_count"] == 1
+    assert summary["ambiguous_group_count"] == 1
+    assert checkout_authority_blocker(
+        project,
+        workspace_root=portfolio_workspace,
+    ) == "checkout-authority-unknown:worktree_enumeration_failed"
+    assert any(
+        "same-origin checkout groups" in warning
+        for warning in result.snapshot.warnings
+    )
+    assert all(
+        "same-origin full-clone groups" not in warning
+        for warning in result.snapshot.warnings
+    )
+    validate_truth_snapshot(result.snapshot)
+
+    markdown = render_portfolio_report_markdown(result.snapshot, "output/x.json")
+    assert "`worktree_enumeration_failed`" in markdown
+    assert "No same-origin checkout collisions were observed." not in markdown
+    validate_portfolio_report_markdown(markdown)
+
+
+def test_external_declared_checkout_is_opaque_unknown(
+    portfolio_workspace: Path,
+    portfolio_catalog: Path,
+    legacy_registry: Path,
+) -> None:
+    repo = portfolio_workspace / "ExternalRepo"
+    repo.mkdir()
+    external_root = portfolio_workspace.parent / "outside"
+    external_root.mkdir()
+    escape = portfolio_workspace / "escape"
+    escape.symlink_to(external_root, target_is_directory=True)
+    external_target = escape / "ExternalRepo" / "src"
+    _write(
+        repo / "AGENTS.md",
+        "# ExternalRepo\n\n## Canonical Paths\n\n"
+        f"- Source: `{external_target}`\n",
+    )
+    subprocess.run(["git", "init", "-q", "-b", "main"], cwd=repo, check=True)
+    subprocess.run(
+        [
+            "git",
+            "remote",
+            "add",
+            "origin",
+            "git@github.com:owner/ExternalRepo.git",
+        ],
+        cwd=repo,
+        check=True,
+    )
+    subprocess.run(["git", "add", "AGENTS.md"], cwd=repo, check=True)
+    subprocess.run(
+        [
+            "git",
+            "-c",
+            "user.name=Test",
+            "-c",
+            "user.email=test@example.invalid",
+            "commit",
+            "-q",
+            "-m",
+            "fixture",
+        ],
+        cwd=repo,
+        check=True,
+    )
+
+    result = build_portfolio_truth_snapshot(
+        workspace_root=portfolio_workspace,
+        catalog_path=portfolio_catalog,
+        legacy_registry_path=legacy_registry,
+        include_notion=False,
+        now=datetime(2026, 8, 3, tzinfo=timezone.utc),
+    )
+
+    project = next(
+        item
+        for item in result.snapshot.projects
+        if item.identity.repo_full_name == "owner/ExternalRepo"
+    )
+    authority = project.repository_state["checkout_authority"]
+    assert authority["selection"]["state"] == "unknown"
+    assert (
+        authority["selection"]["reason_code"]
+        == "declared_checkout_path_unresolved"
+    )
+    assert authority["unresolved_declared_paths"] == ["external-checkout"]
+    assert str(external_target) not in json.dumps(authority)
+    assert str(external_target.resolve()) not in json.dumps(authority)
+    assert checkout_authority_blocker(
+        project,
+        workspace_root=portfolio_workspace,
+    ) == "checkout-authority-unknown:declared_checkout_path_unresolved"
+    validate_truth_snapshot(result.snapshot)
+
+
+def test_external_linked_worktree_flows_through_truth_validation_and_report(
+    portfolio_workspace: Path,
+    portfolio_catalog: Path,
+    legacy_registry: Path,
+) -> None:
+    repo = portfolio_workspace / "ExternalWorktreeRepo"
+    repo.mkdir()
+    _write(repo / "README.md", "# ExternalWorktreeRepo\n")
+    subprocess.run(["git", "init", "-q", "-b", "main"], cwd=repo, check=True)
+    subprocess.run(
+        [
+            "git",
+            "remote",
+            "add",
+            "origin",
+            "git@github.com:owner/ExternalWorktreeRepo.git",
+        ],
+        cwd=repo,
+        check=True,
+    )
+    subprocess.run(["git", "add", "README.md"], cwd=repo, check=True)
+    subprocess.run(
+        [
+            "git",
+            "-c",
+            "user.name=Test",
+            "-c",
+            "user.email=test@example.invalid",
+            "commit",
+            "-q",
+            "-m",
+            "fixture",
+        ],
+        cwd=repo,
+        check=True,
+    )
+    external = (
+        portfolio_workspace.parent
+        / "external-worktree-path-must-not-be-published"
+    )
+    subprocess.run(
+        ["git", "worktree", "add", "-q", "-b", "external", str(external), "HEAD"],
+        cwd=repo,
+        check=True,
+    )
+
+    result = build_portfolio_truth_snapshot(
+        workspace_root=portfolio_workspace,
+        catalog_path=portfolio_catalog,
+        legacy_registry_path=legacy_registry,
+        include_notion=False,
+        now=datetime(2026, 8, 3, tzinfo=timezone.utc),
+    )
+
+    project = next(
+        item
+        for item in result.snapshot.projects
+        if item.identity.repo_full_name == "owner/ExternalWorktreeRepo"
+    )
+    authority = project.repository_state["checkout_authority"]
+    assert authority["checkout_count"] == 2
+    assert authority["full_clone_count"] == 1
+    assert authority["selection"]["state"] == "unknown"
+    assert (
+        authority["selection"]["reason_code"]
+        == "external_linked_worktree_unobserved"
+    )
+    assert authority["discarded_checkouts"] == [
+        {
+            "path": "external-worktree",
+            "state": "unknown",
+            "relation": "linked_worktree",
+            "head": None,
+            "branch": None,
+            "dirty": None,
+            "dirty_path_count": None,
+            "bare": None,
+        }
+    ]
+    assert str(external) not in json.dumps(authority)
+    assert str(external) not in json.dumps(result.snapshot.to_dict())
+    assert checkout_authority_blocker(
+        project,
+        workspace_root=portfolio_workspace,
+    ) == "checkout-authority-unknown:external_linked_worktree_unobserved"
+    validate_truth_snapshot(result.snapshot)
+
+    markdown = render_portfolio_report_markdown(result.snapshot, "output/x.json")
+    assert "`external_linked_worktree_unobserved`" in markdown
+    assert "`external-worktree`: `linked_worktree`" in markdown
+    assert "No same-origin checkout collisions were observed." not in markdown
+    assert str(external) not in markdown
+    validate_portfolio_report_markdown(markdown)
+
+
+def test_prunable_linked_worktree_is_unknown_not_publication_failure(
+    portfolio_workspace: Path,
+    portfolio_catalog: Path,
+    legacy_registry: Path,
+) -> None:
+    repo = portfolio_workspace / "PrunableRepo"
+    repo.mkdir()
+    _write(repo / "README.md", "# PrunableRepo\n")
+    subprocess.run(["git", "init", "-q", "-b", "main"], cwd=repo, check=True)
+    subprocess.run(
+        [
+            "git",
+            "remote",
+            "add",
+            "origin",
+            "git@github.com:owner/PrunableRepo.git",
+        ],
+        cwd=repo,
+        check=True,
+    )
+    subprocess.run(["git", "add", "README.md"], cwd=repo, check=True)
+    subprocess.run(
+        [
+            "git",
+            "-c",
+            "user.name=Test",
+            "-c",
+            "user.email=test@example.invalid",
+            "commit",
+            "-q",
+            "-m",
+            "fixture",
+        ],
+        cwd=repo,
+        check=True,
+    )
+    linked = portfolio_workspace / "_codex-worktrees" / "prunable-repo"
+    linked.parent.mkdir()
+    subprocess.run(
+        ["git", "worktree", "add", "-q", "-b", "feature", str(linked), "HEAD"],
+        cwd=repo,
+        check=True,
+    )
+    preserved = portfolio_workspace / "_backups" / "prunable-repo"
+    preserved.parent.mkdir()
+    linked.rename(preserved)
+
+    result = build_portfolio_truth_snapshot(
+        workspace_root=portfolio_workspace,
+        catalog_path=portfolio_catalog,
+        legacy_registry_path=legacy_registry,
+        include_notion=False,
+        now=datetime(2026, 8, 3, tzinfo=timezone.utc),
+    )
+
+    project = next(
+        item
+        for item in result.snapshot.projects
+        if item.identity.repo_full_name == "owner/PrunableRepo"
+    )
+    authority = project.repository_state["checkout_authority"]
+    assert authority["selection"]["state"] == "unknown"
+    assert authority["selection"]["reason_code"] == "checkout_observation_failed"
+    missing = next(
+        item
+        for item in authority["discarded_checkouts"]
+        if item["path"] == "_codex-worktrees/prunable-repo"
+    )
+    assert missing["state"] == "unknown"
+    assert checkout_authority_blocker(
+        project,
+        workspace_root=portfolio_workspace,
+    ) == "checkout-authority-unknown:checkout_observation_failed"
+    validate_truth_snapshot(result.snapshot)
+
+
+def test_discovered_bare_coordinator_sibling_preserves_identity_and_mutation_path(
+    portfolio_workspace: Path,
+    portfolio_catalog: Path,
+    legacy_registry: Path,
+    monkeypatch,
+) -> None:
+    portfolio_catalog.write_text(
+        """
+defaults:
+  lifecycle_state: maintenance
+  criticality: medium
+  review_cadence: monthly
+  category: default-category
+  tool_provenance: unknown
+
+repos:
+  Repo:
+    owner: coordinator-owner
+    lifecycle_state: active
+    review_cadence: weekly
+    intended_disposition: maintain
+    tool_provenance: codex
+"""
+    )
+    legacy_registry.write_text(
+        """
+# Project Registry
+
+## Standalone Projects (Root Level)
+
+| Project | Status | Tool | Context Quality | Stack | Context Files | Category | Notes |
+|---------|--------|------|-----------------|-------|---------------|----------|-------|
+| Repo | parked | codex | standard | Python | README.md | unknown | Coordinator legacy |
 """
     )
-    return path
-
+    monkeypatch.setattr(
+        "src.portfolio_truth_reconcile.load_safe_notion_project_context",
+        lambda: {
+            "repo": {
+                "portfolio_call": "Maintain",
+                "momentum": "Stable",
+                "current_state": "Coordinator identity retained",
+            }
+        },
+    )
+    seed = portfolio_workspace / "_backups" / "seed"
+    seed.mkdir(parents=True)
+    _write(seed / "README.md", "# Repo\n")
+    subprocess.run(["git", "init", "-q", "-b", "main"], cwd=seed, check=True)
+    subprocess.run(["git", "add", "README.md"], cwd=seed, check=True)
+    subprocess.run(
+        [
+            "git",
+            "-c",
+            "user.name=Test",
+            "-c",
+            "user.email=test@example.invalid",
+            "commit",
+            "-q",
+            "-m",
+            "fixture",
+        ],
+        cwd=seed,
+        check=True,
+    )
+    coordinator = portfolio_workspace / "Repo"
+    subprocess.run(
+        ["git", "clone", "-q", "--bare", str(seed), str(coordinator)],
+        check=True,
+    )
+    subprocess.run(
+        ["git", "remote", "set-url", "origin", "git@github.com:owner/Repo.git"],
+        cwd=coordinator,
+        check=True,
+    )
+    linked = portfolio_workspace / "Repo-main"
+    subprocess.run(
+        ["git", "worktree", "add", "-q", str(linked), "main"],
+        cwd=coordinator,
+        check=True,
+    )
 
-def test_truth_snapshot_respects_declared_and_derived_fields(
-    portfolio_workspace: Path,
-    portfolio_catalog: Path,
-    legacy_registry: Path,
-) -> None:
-    now = datetime.fromtimestamp(1_700_200_000, tz=timezone.utc)
     result = build_portfolio_truth_snapshot(
         workspace_root=portfolio_workspace,
         catalog_path=portfolio_catalog,
         legacy_registry_path=legacy_registry,
-        include_notion=False,
-        now=now,
+        include_notion=True,
+        now=datetime(2026, 8, 3, tzinfo=timezone.utc),
     )
 
-    projects = {
-        project.identity.display_name: project for project in result.snapshot.projects
-    }
-    alpha = projects["Alpha"]
-    beta = projects["Beta"]
-    gamma = projects["Calibrate"]
+    project = next(
+        item
+        for item in result.snapshot.projects
+        if item.identity.repo_full_name == "owner/Repo"
+    )
+    authority = project.repository_state["checkout_authority"]
+    assert project.identity.display_name == "Repo"
+    assert project.identity.path == "Repo"
+    assert project.identity.project_key == "Repo"
+    assert project.declared.owner == "coordinator-owner"
+    assert project.declared.lifecycle_state == "active"
+    assert project.declared.review_cadence == "weekly"
+    assert project.declared.category == "unknown"
+    assert project.advisory.legacy_status == "parked"
+    assert project.advisory.notion_portfolio_call == "Maintain"
+    assert project.advisory.notion_current_state == "Coordinator identity retained"
+    assert authority["selection"]["state"] == "selected"
+    assert authority["canonical_project_path"] == "Repo"
+    assert authority["selection"]["selected_path"] == "Repo-main"
+    assert checkout_authority_path(project) == "Repo-main"
+    assert project.repository_state["local"]["path"] == str(linked)
+    assert checkout_authority_blocker(
+        project,
+        workspace_root=portfolio_workspace,
+    ) is None
+    validate_truth_snapshot(result.snapshot)
 
-    for project in projects.values():
-        assert REQUIRED_PROJECT_PROVENANCE_KEYS <= project.provenance.keys()
+    plan = build_context_recovery_plan(
+        result.snapshot,
+        workspace_root=portfolio_workspace,
+    )
+    target = next(item for item in plan.projects if item.project_key == "Repo")
+    assert target.relative_path == "Repo-main"
+    assert target.target_path.startswith(str(linked))
 
-    assert alpha.identity.project_key == "Alpha"
-    assert alpha.declared.owner == "d"
-    assert alpha.declared.category == "commercial"
-    assert alpha.declared.operating_path == "maintain"
-    assert alpha.derived.context_quality == "full"
-    assert alpha.derived.activity_status == "active"
-    assert alpha.derived.archived is False
-    assert alpha.derived.attention_state == "active-product"
-    assert alpha.derived.primary_context_file == "CLAUDE.md"
-    assert alpha.derived.project_summary_present is True
-    assert alpha.derived.next_recommended_move_present is True
-    assert hasattr(alpha.declared, "doctor_standard")
-    assert hasattr(alpha.declared, "automation_eligible")
-    assert alpha.declared.automation_eligible is False
-    assert hasattr(alpha, "risk")
-    assert alpha.risk.risk_tier in {"elevated", "moderate", "baseline", "deferred"}
 
-    assert beta.identity.section_marker == "ITPRJsViaClaude/"
-    assert beta.declared.category == "it-work"
-    assert beta.derived.context_quality == "boilerplate"
-    assert beta.derived.activity_status == "stale"
-    assert beta.derived.attention_state == "parked"
+def test_bare_coordinator_preserves_nested_canonical_group_policy(
+    tmp_path: Path,
+) -> None:
+    workspace = tmp_path / "workspace"
+    workspace.mkdir()
+    catalog = tmp_path / "portfolio-catalog.yaml"
+    catalog.write_text(
+        """
+defaults:
+  lifecycle_state: maintenance
+  criticality: medium
+  review_cadence: monthly
+  category: default-category
+  tool_provenance: unknown
 
-    assert gamma.identity.section_marker == "iOS Projects"
-    assert gamma.derived.stack == ["Swift"]
+groups:
+  canonical_infra:
+    section_marker: Infra/
+    section_label: Canonical Infrastructure
+    path_prefixes:
+      - Infra
+    owner: canonical-owner
+    lifecycle_state: active
+    review_cadence: weekly
+    category: infrastructure
+    tool_provenance: codex
+  physical_worktrees:
+    section_marker: Physical Worktrees/
+    section_label: Physical Worktrees
+    path_prefixes:
+      - _codex-worktrees
+    owner: wrong-physical-owner
+    lifecycle_state: parked
+    review_cadence: yearly
+    category: vanity
+    tool_provenance: unknown
+"""
+    )
+    registry = tmp_path / "project-registry.md"
+    registry.write_text("# Project Registry\n")
 
-    assert result.snapshot.schema_version == "0.11.0"
-    assert result.snapshot.derivation_policy_version == "portfolio_attention.v3"
-    assert result.snapshot.inputs["catalog"]["sha256"]
-    assert result.snapshot.inputs["notion"]["mode"] == "unavailable"
-    assert result.snapshot.exclusions == {
-        "policy_version": "workspace_discovery.v2",
-        "counts": {},
-    }
-    assert (
-        result.snapshot.source_summary["attention_state_counts"]["active-product"] == 1
+    seed = workspace / "_backups" / "seed"
+    seed.mkdir(parents=True)
+    _write(seed / "README.md", "# Repo\n")
+    subprocess.run(["git", "init", "-q", "-b", "main"], cwd=seed, check=True)
+    subprocess.run(["git", "add", "README.md"], cwd=seed, check=True)
+    subprocess.run(
+        [
+            "git",
+            "-c",
+            "user.name=Test",
+            "-c",
+            "user.email=test@example.invalid",
+            "commit",
+            "-q",
+            "-m",
+            "fixture",
+        ],
+        cwd=seed,
+        check=True,
+    )
+    coordinator = workspace / "Infra" / "Repo"
+    coordinator.parent.mkdir()
+    subprocess.run(
+        ["git", "clone", "-q", "--bare", str(seed), str(coordinator)],
+        check=True,
+    )
+    subprocess.run(
+        ["git", "remote", "set-url", "origin", "git@github.com:owner/Repo.git"],
+        cwd=coordinator,
+        check=True,
+    )
+    linked = workspace / "_codex-worktrees" / "repo-main"
+    linked.parent.mkdir()
+    subprocess.run(
+        ["git", "worktree", "add", "-q", str(linked), "main"],
+        cwd=coordinator,
+        check=True,
     )
-    assert result.snapshot.source_summary["attention_state_counts"]["parked"] == 1
 
-    # Derived rollups are emitted so downstream consumers (command-center) read
-    # them instead of re-deriving the auditor's risk/security logic.
-    snapshot_dict = result.snapshot.to_dict()
-    rollups = snapshot_dict["rollups"]
-    assert set(rollups["risk_tier_counts"]) == {
-        "elevated",
-        "moderate",
-        "baseline",
-        "deferred",
-    }
-    assert sum(rollups["risk_tier_counts"].values()) == len(result.snapshot.projects)
-    assert set(rollups["security"]) == {
-        "scanned_count",
-        "unavailable_count",
-        "complete_repo_count",
-        "partial_repo_count",
-        "stale_count",
-        "unknown_count",
-        "cohort_repository_count",
-        "cohort_complete_count",
-        "cohort_partial_count",
-        "cohort_stale_count",
-        "cohort_unknown_count",
-        "dependabot_observed_count",
-        "code_scanning_observed_count",
-        "secret_scanning_observed_count",
-        "dependabot_zero_finding_count",
-        "code_scanning_zero_finding_count",
-        "secret_scanning_zero_finding_count",
-        "remote_default_branch_observed_count",
-        "remote_default_branch_partial_count",
-        "remote_default_branch_stale_count",
-        "remote_default_branch_unavailable_count",
-        "coverage_state",
-        "repos_with_open_high_critical",
-        "total_open_high",
-        "total_open_critical",
-    }
-    assert rollups["security"]["cohort_repository_count"] == 1
-    assert rollups["security"]["cohort_unknown_count"] == 1
-    assert rollups["security"]["cohort_complete_count"] == 0
-    assert set(rollups["decision"]) == {
-        "decision_needed_count",
-        "default_attention_count",
-    }
-    assert (
-        rollups["decision"]["default_attention_count"]
-        >= rollups["decision"]["decision_needed_count"]
+    result = build_portfolio_truth_snapshot(
+        workspace_root=workspace,
+        catalog_path=catalog,
+        legacy_registry_path=registry,
+        include_notion=False,
+        now=datetime(2026, 8, 3, tzinfo=timezone.utc),
     )
-    # Per-project open_high_critical is emitted in the security block.
-    assert "open_high_critical" in snapshot_dict["projects"][0]["security"]
+
+    project = next(
+        item
+        for item in result.snapshot.projects
+        if item.identity.repo_full_name == "owner/Repo"
+    )
+    authority = project.repository_state["checkout_authority"]
+    assert project.identity.path == "Infra/Repo"
+    assert project.identity.group_key == "canonical_infra"
+    assert project.identity.section_marker == "Infra/"
+    assert project.identity.section_label == "Canonical Infrastructure"
+    assert project.declared.owner == "canonical-owner"
+    assert project.declared.lifecycle_state == "active"
+    assert project.declared.review_cadence == "weekly"
+    assert project.declared.category == "infrastructure"
+    assert project.declared.owner != "wrong-physical-owner"
+    assert authority["canonical_project_path"] == "Infra/Repo"
+    assert authority["selection"]["selected_path"] == (
+        "_codex-worktrees/repo-main"
+    )
+    assert checkout_authority_path(project) == "_codex-worktrees/repo-main"
+    assert project.repository_state["local"]["path"] == str(linked)
+    assert checkout_authority_blocker(project, workspace_root=workspace) is None
+    validate_truth_snapshot(result.snapshot)
 
 
 def test_live_catalog_produces_exact_tier_zero_attention_semantics(
@@ -4813,6 +5776,7 @@ def test_report_subcommand_parses_security_cohort_count() -> None:
 def test_portfolio_truth_app_threads_security_cohort_count(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
+    capsys: pytest.CaptureFixture[str],
 ) -> None:
     from types import SimpleNamespace
 
@@ -4835,6 +5799,9 @@ def fake_publish(**kwargs):
             project_count=0,
             registry_changed=False,
             report_changed=False,
+            checkout_collision_group_count=2,
+            checkout_authority_unknown_count=1,
+            discarded_checkout_count=4,
         )
 
     monkeypatch.setattr(
@@ -5229,6 +6196,175 @@ def test_context_recovery_plan_freezes_and_filters_targets(
     assert targets["tmp-scaffold"].reason == "temporary-or-generated"
 
 
+def test_context_recovery_plan_skips_unknown_checkout_authority(
+    portfolio_workspace: Path,
+    portfolio_catalog: Path,
+    legacy_registry: Path,
+) -> None:
+    target_repo = portfolio_workspace / "FreshCollision"
+    target_repo.mkdir()
+    _write(target_repo / "README.md", "# FreshCollision\n\nFresh repo.\n")
+
+    result = build_portfolio_truth_snapshot(
+        workspace_root=portfolio_workspace,
+        catalog_path=portfolio_catalog,
+        legacy_registry_path=legacy_registry,
+        include_notion=False,
+        now=datetime.fromtimestamp(1_700_000_100, tz=timezone.utc),
+    )
+    projects = [
+        replace(
+            project,
+            repository_state={
+                **project.repository_state,
+                "checkout_authority": _checkout_authority_fixture(
+                    canonical_path=project.identity.path,
+                    origin=project.identity.repo_full_name or "fixture/FreshCollision",
+                    state="unknown",
+                    reason_code="conflicting_full_clone_heads",
+                ),
+            },
+        )
+        if project.identity.project_key == "FreshCollision"
+        else project
+        for project in result.snapshot.projects
+    ]
+    snapshot = replace(result.snapshot, projects=projects)
+
+    plan = build_context_recovery_plan(snapshot, workspace_root=portfolio_workspace)
+    target = next(
+        item for item in plan.projects if item.project_key == "FreshCollision"
+    )
+
+    assert target.status == "skipped"
+    assert target.reason == "checkout-authority-unknown:conflicting_full_clone_heads"
+
+
+def test_context_recovery_malformed_authority_never_redirects_target_path(
+    portfolio_workspace: Path,
+    portfolio_catalog: Path,
+    legacy_registry: Path,
+) -> None:
+    target_repo = portfolio_workspace / "FreshMalformed"
+    target_repo.mkdir()
+    _write(target_repo / "README.md", "# FreshMalformed\n\nFresh repo.\n")
+
+    result = build_portfolio_truth_snapshot(
+        workspace_root=portfolio_workspace,
+        catalog_path=portfolio_catalog,
+        legacy_registry_path=legacy_registry,
+        include_notion=False,
+        now=datetime.fromtimestamp(1_700_000_100, tz=timezone.utc),
+    )
+    projects = [
+        replace(
+            project,
+            repository_state={
+                **project.repository_state,
+                "checkout_authority": {
+                    "schema_version": "CheckoutCollisionV1",
+                    "selection": {
+                        "state": "selected",
+                        "reason_code": "single_clone_topology",
+                        "representative_path": "_codex-worktrees/malicious-target",
+                        "selected_path": "_codex-worktrees/malicious-target",
+                    },
+                    "checkouts": [
+                        {
+                            "path": "_codex-worktrees/malicious-target",
+                            "state": "observed",
+                            "relation": "representative",
+                            "bare": False,
+                        }
+                    ],
+                },
+            },
+        )
+        if project.identity.project_key == "FreshMalformed"
+        else project
+        for project in result.snapshot.projects
+    ]
+    snapshot = replace(result.snapshot, projects=projects)
+
+    plan = build_context_recovery_plan(snapshot, workspace_root=portfolio_workspace)
+    target = next(
+        item for item in plan.projects if item.project_key == "FreshMalformed"
+    )
+
+    assert target.status == "skipped"
+    assert target.reason == "checkout-authority-malformed"
+    assert target.relative_path == "FreshMalformed"
+    assert target.target_path.startswith(str(target_repo))
+    assert "malicious-target" not in target.target_path
+
+
+def test_checkout_authority_path_falls_back_for_malformed_envelope_variants() -> None:
+    variants = []
+
+    missing_field = _checkout_authority_fixture(
+        canonical_path="Repo", origin="owner/Repo"
+    )
+    missing_field.pop("origin")
+    variants.append(missing_field)
+
+    invalid_type = _checkout_authority_fixture(
+        canonical_path="Repo", origin="owner/Repo"
+    )
+    invalid_type["selection"] = "selected"
+    variants.append(invalid_type)
+
+    invalid_count = _checkout_authority_fixture(
+        canonical_path="Repo", origin="owner/Repo"
+    )
+    invalid_count["checkout_count"] = 3
+    variants.append(invalid_count)
+
+    malformed_record = _checkout_authority_fixture(
+        canonical_path="Repo", origin="owner/Repo"
+    )
+    del malformed_record["checkouts"][0]["head"]
+    variants.append(malformed_record)
+
+    unknown_discarded = _checkout_authority_fixture(
+        canonical_path="Repo", origin="owner/Repo"
+    )
+    unknown_discarded["checkouts"][1].update(
+        {
+            "state": "unknown",
+            "head": None,
+            "branch": None,
+            "dirty": None,
+            "dirty_path_count": None,
+            "bare": None,
+        }
+    )
+    variants.append(unknown_discarded)
+
+    dirty_discarded = _checkout_authority_fixture(
+        canonical_path="Repo", origin="owner/Repo"
+    )
+    dirty_discarded["checkouts"][1].update(
+        {"dirty": True, "dirty_path_count": 1}
+    )
+    variants.append(dirty_discarded)
+
+    for authority in variants:
+        project = {
+            "identity": {"path": "Repo", "repo_full_name": "owner/Repo"},
+            "repository_state": {
+                "checkout_authority": deepcopy(authority),
+            },
+        }
+        with pytest.raises(ValueError):
+            validate_checkout_authority_envelope(
+                authority,
+                identity_path="Repo",
+                repo_full_name="owner/Repo",
+            )
+        assert checkout_authority_path(project) == "Repo"
+        assert checkout_authority_blocker(project) == "checkout-authority-malformed"
+
+
 def test_context_recovery_apply_writes_primary_context_and_catalog_seed(
     portfolio_workspace: Path,
     portfolio_catalog: Path,
diff --git a/tests/test_portfolio_truth_contract_fixture.py b/tests/test_portfolio_truth_contract_fixture.py
index afae89a9..0fe44795 100644
--- a/tests/test_portfolio_truth_contract_fixture.py
+++ b/tests/test_portfolio_truth_contract_fixture.py
@@ -30,6 +30,7 @@
     manifest_bytes,
 )
 from src.portfolio_truth_reconcile import _build_security_fields
+from src.portfolio_truth_sources import WORKSPACE_DISCOVERY_POLICY_VERSION
 from src.portfolio_truth_types import SCHEMA_VERSION
 from src.portfolio_truth_validate import (
     _snapshot_from_payload,
@@ -100,7 +101,7 @@ def test_fixture_spans_the_receipt_states_with_additive_canaries() -> None:
         },
     }
     assert fixture["exclusions"] == {
-        "policy_version": "workspace_discovery.v2",
+        "policy_version": WORKSPACE_DISCOVERY_POLICY_VERSION,
         "counts": {},
     }
     assert sorted(states) == ["complete", "partial", "stale", "unknown"]
diff --git a/tests/test_portfolio_truth_sources.py b/tests/test_portfolio_truth_sources.py
index 42b31fdb..ad427f16 100644
--- a/tests/test_portfolio_truth_sources.py
+++ b/tests/test_portfolio_truth_sources.py
@@ -10,18 +10,50 @@
 
 import subprocess
 from datetime import datetime, timezone
+from pathlib import Path
 
 from src.portfolio_truth_sources import (
     WORKSPACE_EXCLUSION_REASONS,
     _dedupe_checkouts_by_origin,
     _is_ignored_project_dir,
+    checkout_collision_summary,
     discover_workspace_projects,
     workspace_exclusion_reason,
 )
 
 
-def _p(name: str, repo_full_name: str = "", path: str | None = None) -> dict:
-    return {"name": name, "repo_full_name": repo_full_name, "path": path or name}
+def _p(
+    name: str,
+    repo_full_name: str = "",
+    path: str | None = None,
+    *,
+    head: str | None = None,
+    branch: str | None = "main",
+    common_dir: str | None = None,
+    dirty: bool | None = False,
+    dirty_path_count: int | None = 0,
+    bare: bool = False,
+    declared_paths: list[dict[str, str]] | None = None,
+) -> dict:
+    relative_path = path or name
+    project = {
+        "name": name,
+        "repo_full_name": repo_full_name,
+        "path": relative_path,
+        "project_path": Path("/workspace") / relative_path,
+    }
+    if head is not None or common_dir is not None:
+        project["_checkout_observation"] = {
+            "state": "observed",
+            "head": head,
+            "branch": branch,
+            "dirty": dirty,
+            "dirty_path_count": dirty_path_count,
+            "git_common_dir": common_dir,
+            "bare": bare,
+            "declared_paths": declared_paths or [],
+        }
+    return project
 
 
 def test_collapses_same_origin_checkouts_to_one() -> None:
@@ -87,6 +119,403 @@ def test_result_is_sorted_by_name_case_insensitively() -> None:
     assert [p["name"] for p in result] == ["Alpha", "mike", "zeta"]
 
 
+def test_linked_worktrees_keep_discarded_checkout_evidence() -> None:
+    collisions: list[dict] = []
+    head = "1" * 40
+    discovered = [
+        _p(
+            "Repo",
+            "owner/Repo",
+            head=head,
+            common_dir="/git/Repo/.git",
+        ),
+        _p(
+            "Repo-fix",
+            "owner/Repo",
+            head="2" * 40,
+            branch="fix",
+            common_dir="/git/Repo/.git",
+        ),
+    ]
+
+    result = _dedupe_checkouts_by_origin(
+        discovered,
+        checkout_collisions=collisions,
+    )
+
+    assert len(result) == 1
+    assert len(collisions) == 1
+    collision = collisions[0]
+    assert collision["selection"]["state"] == "selected"
+    assert collision["selection"]["reason_code"] == "single_clone_topology"
+    assert collision["full_clone_count"] == 1
+    assert collision["discarded_checkouts"] == [
+        {
+            "path": "Repo-fix",
+            "state": "observed",
+            "relation": "linked_worktree",
+            "head": "2" * 40,
+            "branch": "fix",
+            "dirty": False,
+            "dirty_path_count": 0,
+            "bare": False,
+        }
+    ]
+
+
+def test_conflicting_independent_full_clone_heads_are_unknown() -> None:
+    collisions: list[dict] = []
+    discovered = [
+        _p(
+            "Repo",
+            "owner/Repo",
+            head="1" * 40,
+            common_dir="/git/Repo/.git",
+        ),
+        _p(
+            "Archive/Repo",
+            "owner/Repo",
+            path="Archive/Repo",
+            head="2" * 40,
+            common_dir="/git/Archive/Repo/.git",
+        ),
+    ]
+
+    result = _dedupe_checkouts_by_origin(
+        discovered,
+        checkout_collisions=collisions,
+    )
+
+    assert len(result) == 1
+    collision = collisions[0]
+    assert collision["full_clone_count"] == 2
+    assert collision["selection"]["state"] == "unknown"
+    assert collision["selection"]["selected_path"] is None
+    assert collision["selection"]["reason_code"] == "conflicting_full_clone_heads"
+    assert collision["discarded_checkouts"][0]["relation"] == "independent_full_clone"
+
+    summary = checkout_collision_summary(collisions)
+    assert summary["state"] == "unknown"
+    assert summary["group_count"] == 1
+    assert summary["full_clone_group_count"] == 1
+    assert summary["ambiguous_group_count"] == 1
+    assert summary["discarded_checkout_count"] == 1
+
+
+def test_dirty_linked_worktree_in_independent_clone_is_unknown() -> None:
+    collisions: list[dict] = []
+    head = "1" * 40
+    discovered = [
+        _p(
+            "Repo",
+            "owner/Repo",
+            head=head,
+            common_dir="/git/Repo/.git",
+        ),
+        _p(
+            "Repo",
+            "owner/Repo",
+            path="Archive/Repo",
+            head=head,
+            common_dir="/git/Archive/Repo/.git",
+        ),
+        _p(
+            "Repo-fix",
+            "owner/Repo",
+            path="Archive/Repo-fix",
+            head="2" * 40,
+            branch="fix",
+            common_dir="/git/Archive/Repo/.git",
+            dirty=True,
+            dirty_path_count=1,
+        ),
+    ]
+
+    _dedupe_checkouts_by_origin(discovered, checkout_collisions=collisions)
+
+    collision = collisions[0]
+    assert collision["full_clone_count"] == 2
+    assert collision["selection"]["state"] == "unknown"
+    assert collision["selection"]["selected_path"] is None
+    assert collision["selection"]["reason_code"] == "full_clone_local_work_present"
+    assert any(
+        checkout["path"] == "Archive/Repo-fix" and checkout["dirty"] is True
+        for checkout in collision["discarded_checkouts"]
+    )
+
+
+def test_working_checkout_is_preferred_over_bare_same_origin_repo() -> None:
+    collisions: list[dict] = []
+    head = "1" * 40
+    discovered = [
+        _p(
+            "Repo",
+            "owner/Repo",
+            head=head,
+            common_dir="/git/Repo.git",
+            bare=True,
+            dirty=None,
+            dirty_path_count=None,
+        ),
+        _p(
+            "Repo",
+            "owner/Repo",
+            path="Archive/Repo",
+            head=head,
+            common_dir="/git/Archive/Repo/.git",
+        ),
+    ]
+
+    result = _dedupe_checkouts_by_origin(
+        discovered,
+        checkout_collisions=collisions,
+    )
+
+    assert result[0]["path"] == "Repo"
+    assert result[0]["project_path"] == Path("/workspace/Archive/Repo")
+    collision = collisions[0]
+    assert collision["selection"]["state"] == "selected"
+    assert collision["selection"]["selected_path"] == "Archive/Repo"
+    assert collision["checkouts"] == [
+        {
+            "path": "Archive/Repo",
+            "state": "observed",
+            "relation": "representative",
+            "head": head,
+            "branch": "main",
+            "dirty": False,
+            "dirty_path_count": 0,
+            "bare": False,
+        },
+        {
+            "path": "Repo",
+            "state": "observed",
+            "relation": "independent_full_clone",
+            "head": head,
+            "branch": "main",
+            "dirty": None,
+            "dirty_path_count": None,
+            "bare": True,
+        },
+    ]
+
+
+def test_observed_checkout_supplies_evidence_without_replacing_basename_identity() -> None:
+    collisions: list[dict] = []
+    head = "1" * 40
+    discovered = [
+        _p("Repo", "owner/Repo"),
+        _p(
+            "Repo",
+            "owner/Repo",
+            path="Archive/Repo",
+            head=head,
+            common_dir="/git/Archive/Repo/.git",
+        ),
+    ]
+
+    result = _dedupe_checkouts_by_origin(
+        discovered,
+        checkout_collisions=collisions,
+    )
+
+    assert result[0]["path"] == "Repo"
+    assert result[0]["project_path"] == Path("/workspace/Archive/Repo")
+    collision = collisions[0]
+    assert collision["selection"]["state"] == "unknown"
+    assert collision["selection"]["reason_code"] == "checkout_observation_failed"
+    assert collision["selection"]["representative_path"] == "Archive/Repo"
+
+
+def test_discovered_linked_worktree_preserves_coordinator_catalog_identity() -> None:
+    collisions: list[dict] = []
+    head = "1" * 40
+    coordinator = _p(
+        "Repo",
+        "owner/Repo",
+        head=head,
+        common_dir="/git/Repo.git",
+        bare=True,
+        dirty=None,
+        dirty_path_count=None,
+    )
+    coordinator.update(
+        {
+            "group_entry": {"owner": "coordinator-owner"},
+            "source": "coordinator-source",
+        }
+    )
+    linked = _p(
+        "Repo-main",
+        "owner/Repo",
+        head=head,
+        common_dir="/git/Repo.git",
+    )
+    linked.update(
+        {
+            "group_entry": {"owner": "linked-owner"},
+            "source": "linked-source",
+        }
+    )
+
+    result = _dedupe_checkouts_by_origin(
+        [coordinator, linked],
+        checkout_collisions=collisions,
+    )
+
+    assert result[0]["name"] == "Repo"
+    assert result[0]["path"] == "Repo"
+    assert result[0]["group_entry"] == {"owner": "coordinator-owner"}
+    assert result[0]["source"] == "coordinator-source"
+    assert result[0]["project_path"] == Path("/workspace/Repo-main")
+    assert collisions[0]["selection"]["selected_path"] == "Repo-main"
+
+
+def test_declared_bare_singleton_is_unknown() -> None:
+    declaration = {
+        "absolute_path": "/workspace/Repo",
+        "workspace_relative_path": "Repo",
+        "source_file": "AGENTS.md",
+    }
+    collisions: list[dict] = []
+    discovered = [
+        _p(
+            "Repo",
+            "owner/Repo",
+            head="1" * 40,
+            common_dir="/git/Repo.git",
+            bare=True,
+            dirty=None,
+            dirty_path_count=None,
+            declared_paths=[declaration],
+        )
+    ]
+
+    _dedupe_checkouts_by_origin(discovered, checkout_collisions=collisions)
+
+    assert len(collisions) == 1
+    collision = collisions[0]
+    assert collision["checkout_count"] == 1
+    assert collision["selection"]["state"] == "unknown"
+    assert collision["selection"]["selected_path"] is None
+    assert collision["selection"]["reason_code"] == "bare_representative_unusable"
+
+
+def test_declared_linked_worktree_conflicts_with_representative() -> None:
+    declaration = {
+        "absolute_path": "/workspace/Repo-fix/src",
+        "workspace_relative_path": "Repo-fix/src",
+        "source_file": "AGENTS.md",
+    }
+    collisions: list[dict] = []
+    head = "1" * 40
+    discovered = [
+        _p(
+            "Repo",
+            "owner/Repo",
+            head=head,
+            common_dir="/git/Repo/.git",
+            declared_paths=[declaration],
+        ),
+        _p(
+            "Repo-fix",
+            "owner/Repo",
+            head=head,
+            branch="fix",
+            common_dir="/git/Repo/.git",
+            declared_paths=[declaration],
+        ),
+    ]
+
+    _dedupe_checkouts_by_origin(discovered, checkout_collisions=collisions)
+
+    collision = collisions[0]
+    assert collision["full_clone_count"] == 1
+    assert collision["declared_checkout_paths"] == ["Repo-fix"]
+    assert collision["selection"]["state"] == "unknown"
+    assert collision["selection"]["selected_path"] is None
+    assert (
+        collision["selection"]["reason_code"]
+        == "declared_path_conflicts_with_representative"
+    )
+
+
+def test_declared_undiscovered_checkout_is_unknown() -> None:
+    declaration = {
+        "absolute_path": "/workspace/_codex-worktrees/repo-retired/src",
+        "workspace_relative_path": "_codex-worktrees/repo-retired/src",
+        "source_file": "AGENTS.md",
+    }
+    collisions: list[dict] = []
+    discovered = [
+        _p(
+            "Repo",
+            "owner/Repo",
+            head="1" * 40,
+            common_dir="/git/Repo/.git",
+            declared_paths=[declaration],
+        )
+    ]
+
+    _dedupe_checkouts_by_origin(discovered, checkout_collisions=collisions)
+
+    assert len(collisions) == 1
+    collision = collisions[0]
+    assert collision["checkout_count"] == 1
+    assert collision["selection"]["state"] == "unknown"
+    assert collision["selection"]["selected_path"] is None
+    assert collision["selection"]["reason_code"] == "declared_checkout_path_unresolved"
+    assert collision["unresolved_declared_paths"] == [
+        "_codex-worktrees/repo-retired/src"
+    ]
+
+
+def test_declared_path_to_other_full_clone_overrides_head_reason() -> None:
+    nested_declaration = {
+        "absolute_path": "/workspace/Money/AIGCCore/src",
+        "workspace_relative_path": "Money/AIGCCore/src",
+        "source_file": "AGENTS.md",
+    }
+    collisions: list[dict] = []
+    discovered = [
+        _p(
+            "AIGCCore",
+            "owner/AIGCCore",
+            head="1" * 40,
+            common_dir="/git/AIGCCore/.git",
+            declared_paths=[nested_declaration],
+        ),
+        _p(
+            "AIGCCore",
+            "owner/AIGCCore",
+            path="Money/AIGCCore",
+            head="2" * 40,
+            common_dir="/git/Money/AIGCCore/.git",
+            declared_paths=[nested_declaration],
+        ),
+    ]
+
+    _dedupe_checkouts_by_origin(discovered, checkout_collisions=collisions)
+
+    collision = collisions[0]
+    assert collision["selection"]["state"] == "unknown"
+    assert (
+        collision["selection"]["reason_code"]
+        == "declared_path_conflicts_with_representative"
+    )
+    assert collision["declared_checkout_paths"] == ["Money/AIGCCore"]
+    assert collision["declared_path_evidence"] == [
+        {
+            "source_path": "AIGCCore/AGENTS.md",
+            "target_checkout_path": "Money/AIGCCore",
+        },
+        {
+            "source_path": "Money/AIGCCore/AGENTS.md",
+            "target_checkout_path": "Money/AIGCCore",
+        },
+    ]
+
+
 # --- discovery ignore-list: transient / non-project directories ---
 # NoGoPRJs (operator-flagged never-pursued), `*-smoke-export` (generated
 # AuraForge bundles), and `*-tmp-<ts>` clones are scratch artifacts, not real
@@ -216,3 +645,282 @@ def test_discovery_recognizes_conventional_bare_coordinator(tmp_path) -> None:
     project = next(item for item in result if item["name"] == coordinator.name)
     assert project["has_git"] is True
     assert project["project_path"] == coordinator
+    assert project["_checkout_observation"]["state"] == "observed"
+    assert project["_checkout_observation"]["head"] is None
+    assert project["_checkout_observation"]["git_common_dir"] == str(coordinator)
+    assert project["_checkout_observation"]["bare"] is True
+
+
+def test_discovery_observes_dirty_worktree_inside_excluded_container(
+    tmp_path: Path,
+) -> None:
+    repo = tmp_path / "Repo"
+    repo.mkdir()
+    subprocess.run(["git", "init", "-q", "-b", "main"], cwd=repo, check=True)
+    subprocess.run(
+        ["git", "remote", "add", "origin", "git@github.com:owner/Repo.git"],
+        cwd=repo,
+        check=True,
+    )
+    (repo / "README.md").write_text("# Repo\n")
+    subprocess.run(["git", "add", "README.md"], cwd=repo, check=True)
+    subprocess.run(
+        [
+            "git",
+            "-c",
+            "user.name=Test",
+            "-c",
+            "user.email=test@example.invalid",
+            "commit",
+            "-q",
+            "-m",
+            "fixture",
+        ],
+        cwd=repo,
+        check=True,
+    )
+    linked = tmp_path / "_codex-worktrees" / "repo-feature"
+    linked.parent.mkdir()
+    subprocess.run(
+        ["git", "worktree", "add", "-q", "-b", "feature", str(linked), "HEAD"],
+        cwd=repo,
+        check=True,
+    )
+    (linked / "preserve.txt").write_text("dirty\n")
+
+    collisions: list[dict] = []
+    exclusions: dict[str, int] = {}
+    projects = discover_workspace_projects(
+        tmp_path,
+        catalog_data={},
+        now=datetime(2026, 8, 3, tzinfo=timezone.utc),
+        checkout_collisions=collisions,
+        exclusion_counts=exclusions,
+    )
+
+    repo_projects = [
+        project for project in projects if project["repo_full_name"] == "owner/Repo"
+    ]
+    assert len(repo_projects) == 1
+    assert repo_projects[0]["path"] == "Repo"
+    assert exclusions["linked-worktree-container"] == 1
+    collision = collisions[0]
+    assert collision["checkout_count"] == 2
+    assert collision["full_clone_count"] == 1
+    assert collision["selection"]["state"] == "unknown"
+    assert (
+        collision["selection"]["reason_code"]
+        == "linked_worktree_local_work_present"
+    )
+    linked_evidence = next(
+        item
+        for item in collision["discarded_checkouts"]
+        if item["path"] == "_codex-worktrees/repo-feature"
+    )
+    assert linked_evidence["relation"] == "linked_worktree"
+    assert linked_evidence["dirty"] is True
+
+
+def test_discovery_preserves_opaque_external_linked_worktree_evidence(
+    tmp_path: Path,
+) -> None:
+    workspace = tmp_path / "workspace"
+    workspace.mkdir()
+    repo = workspace / "Repo"
+    repo.mkdir()
+    subprocess.run(["git", "init", "-q", "-b", "main"], cwd=repo, check=True)
+    subprocess.run(
+        ["git", "remote", "add", "origin", "git@github.com:owner/Repo.git"],
+        cwd=repo,
+        check=True,
+    )
+    (repo / "README.md").write_text("# Repo\n")
+    subprocess.run(["git", "add", "README.md"], cwd=repo, check=True)
+    subprocess.run(
+        [
+            "git",
+            "-c",
+            "user.name=Test",
+            "-c",
+            "user.email=test@example.invalid",
+            "commit",
+            "-q",
+            "-m",
+            "fixture",
+        ],
+        cwd=repo,
+        check=True,
+    )
+    external = tmp_path / "external-worktree-path-must-not-be-published"
+    subprocess.run(
+        ["git", "worktree", "add", "-q", "-b", "external", str(external), "HEAD"],
+        cwd=repo,
+        check=True,
+    )
+
+    collisions: list[dict] = []
+    projects = discover_workspace_projects(
+        workspace,
+        catalog_data={},
+        now=datetime(2026, 8, 3, tzinfo=timezone.utc),
+        checkout_collisions=collisions,
+    )
+
+    assert len(projects) == 1
+    collision = collisions[0]
+    assert collision["checkout_count"] == 2
+    assert collision["full_clone_count"] == 1
+    assert collision["selection"]["state"] == "unknown"
+    assert (
+        collision["selection"]["reason_code"]
+        == "external_linked_worktree_unobserved"
+    )
+    external_evidence = next(
+        item
+        for item in collision["discarded_checkouts"]
+        if item["path"] == "external-worktree"
+    )
+    assert external_evidence["state"] == "unknown"
+    assert external_evidence["relation"] == "linked_worktree"
+    assert str(external) not in repr(collision)
+
+    summary = checkout_collision_summary(collisions)
+    assert summary["state"] == "unknown"
+    assert summary["group_count"] == 1
+    assert summary["ambiguous_group_count"] == 1
+    assert summary["discarded_checkout_count"] == 1
+
+
+def test_bare_coordinator_uses_worktree_inside_excluded_container(
+    tmp_path: Path,
+) -> None:
+    seed = tmp_path / "_backups" / "seed"
+    seed.mkdir(parents=True)
+    subprocess.run(["git", "init", "-q", "-b", "main"], cwd=seed, check=True)
+    (seed / "README.md").write_text("# Repo\n")
+    subprocess.run(["git", "add", "README.md"], cwd=seed, check=True)
+    subprocess.run(
+        [
+            "git",
+            "-c",
+            "user.name=Test",
+            "-c",
+            "user.email=test@example.invalid",
+            "commit",
+            "-q",
+            "-m",
+            "fixture",
+        ],
+        cwd=seed,
+        check=True,
+    )
+    coordinator = tmp_path / "Repo"
+    subprocess.run(
+        ["git", "clone", "-q", "--bare", str(seed), str(coordinator)],
+        check=True,
+    )
+    subprocess.run(
+        ["git", "remote", "set-url", "origin", "git@github.com:owner/Repo.git"],
+        cwd=coordinator,
+        check=True,
+    )
+    linked = tmp_path / "_codex-worktrees" / "repo-main"
+    linked.parent.mkdir()
+    subprocess.run(
+        ["git", "worktree", "add", "-q", str(linked), "main"],
+        cwd=coordinator,
+        check=True,
+    )
+
+    collisions: list[dict] = []
+    projects = discover_workspace_projects(
+        tmp_path,
+        catalog_data={},
+        now=datetime(2026, 8, 3, tzinfo=timezone.utc),
+        checkout_collisions=collisions,
+    )
+
+    repo_projects = [
+        project for project in projects if project["repo_full_name"] == "owner/Repo"
+    ]
+    assert len(repo_projects) == 1
+    assert repo_projects[0]["name"] == "Repo"
+    assert repo_projects[0]["path"] == "Repo"
+    assert repo_projects[0]["project_path"] == linked
+    collision = collisions[0]
+    assert collision["selection"]["state"] == "selected"
+    assert collision["canonical_project_path"] == "Repo"
+    assert collision["selection"]["representative_path"] == (
+        "_codex-worktrees/repo-main"
+    )
+    representative = next(
+        item for item in collision["checkouts"] if item["relation"] == "representative"
+    )
+    assert representative["bare"] is False
+
+
+def test_discovery_observes_conflicting_full_clones_without_count_inflation(
+    tmp_path,
+) -> None:
+    root_clone = tmp_path / "Widget"
+    nested_clone = tmp_path / "Archive" / "Widget"
+    for index, clone in enumerate((root_clone, nested_clone), start=1):
+        clone.mkdir(parents=True)
+        (clone / "README.md").write_text(f"# Widget {index}\n")
+        if clone == root_clone:
+            (clone / "AGENTS.md").write_text(
+                "# Instructions\n\n## Canonical Paths\n\n"
+                f"- Source: `{nested_clone / 'src'}`\n"
+            )
+        subprocess.run(
+            ["git", "init", "-q", "-b", "main"],
+            cwd=clone,
+            check=True,
+        )
+        subprocess.run(
+            ["git", "remote", "add", "origin", "git@github.com:owner/Widget.git"],
+            cwd=clone,
+            check=True,
+        )
+        subprocess.run(["git", "add", "."], cwd=clone, check=True)
+        subprocess.run(
+            [
+                "git",
+                "-c",
+                "user.name=Test",
+                "-c",
+                "user.email=test@example.invalid",
+                "commit",
+                "-q",
+                "-m",
+                f"fixture {index}",
+            ],
+            cwd=clone,
+            check=True,
+        )
+
+    collisions: list[dict] = []
+    projects = discover_workspace_projects(
+        tmp_path,
+        catalog_data={},
+        now=datetime(2026, 8, 3, tzinfo=timezone.utc),
+        checkout_collisions=collisions,
+    )
+
+    widget_projects = [
+        project for project in projects if project["repo_full_name"] == "owner/Widget"
+    ]
+    assert len(widget_projects) == 1
+    assert widget_projects[0]["path"] == "Widget"
+    assert len(collisions) == 1
+    collision = collisions[0]
+    assert collision["checkout_count"] == 2
+    assert collision["full_clone_count"] == 2
+    assert collision["selection"]["state"] == "unknown"
+    assert (
+        collision["selection"]["reason_code"]
+        == "declared_path_conflicts_with_representative"
+    )
+    assert collision["declared_checkout_paths"] == ["Archive/Widget"]
+    assert all(checkout["state"] == "observed" for checkout in collision["checkouts"])
+    assert all(len(checkout["head"]) == 40 for checkout in collision["checkouts"])
diff --git a/tests/test_run_instructions_audit.py b/tests/test_run_instructions_audit.py
index c477601f..24aaf6cb 100644
--- a/tests/test_run_instructions_audit.py
+++ b/tests/test_run_instructions_audit.py
@@ -1,3 +1,4 @@
+from copy import deepcopy
 import json
 import os
 import subprocess
@@ -66,6 +67,64 @@ def _project(key, quality, *, archived=False, path=None):
     }
 
 
+def _checkout_authority(
+    *,
+    canonical_path: str,
+    representative_path: str | None = None,
+    state: str = "selected",
+    reason_code: str = "single_clone_topology",
+) -> dict:
+    representative_path = representative_path or canonical_path
+    representative = {
+        "path": representative_path,
+        "state": "observed",
+        "relation": "representative",
+        "head": "1" * 40,
+        "branch": "main",
+        "dirty": False,
+        "dirty_path_count": 0,
+        "bare": False,
+    }
+    other = {
+        "path": (
+            canonical_path
+            if representative_path != canonical_path
+            else f"{canonical_path}-linked"
+        )
+        if state == "selected"
+        else f"Archive/{canonical_path}",
+        "state": "observed",
+        "relation": (
+            "linked_worktree" if state == "selected" else "independent_full_clone"
+        ),
+        "head": ("1" if state == "selected" else "2") * 40,
+        "branch": "feature",
+        "dirty": False,
+        "dirty_path_count": 0,
+        "bare": False,
+    }
+    return {
+        "schema_version": "CheckoutCollisionV1",
+        "origin": f"owner/{canonical_path.rsplit('/', 1)[-1]}",
+        "canonical_project_path": canonical_path,
+        "checkout_count": 2,
+        "full_clone_count": 1 if state == "selected" else 2,
+        "declared_checkout_paths": [],
+        "declared_path_evidence": [],
+        "unresolved_declared_paths": [],
+        "selection": {
+            "state": state,
+            "reason_code": reason_code,
+            "reason": "fixture authority",
+            "representative_path": representative_path,
+            "selected_path": representative_path if state == "selected" else None,
+            "rationale": "fixture selection",
+        },
+        "checkouts": [representative, other],
+        "discarded_checkouts": [other],
+    }
+
+
 def test_select_pilot_stratifies_sorts_and_filters():
     projects = (
         [_project(f"b{i}", "boilerplate") for i in range(6)]
@@ -128,6 +187,32 @@ def test_build_record_prefers_claude_md():
     assert build_record(project, "/w")["primary_file_name"] == "CLAUDE.md"
 
 
+def test_build_record_uses_selected_checkout_without_replacing_identity():
+    project = {
+        "identity": {
+            "project_key": "Repo",
+            "path": "Repo",
+            "display_name": "Repo",
+        },
+        "derived": {
+            "context_files": ["AGENTS.md"],
+            "run_instructions_present": True,
+        },
+        "repository_state": {
+            "checkout_authority": _checkout_authority(
+                canonical_path="Repo",
+                representative_path="_codex-worktrees/repo-main",
+            )
+        },
+    }
+
+    record = build_record(project, "/workspace")
+
+    assert record["project_key"] == "Repo"
+    assert record["display_name"] == "Repo"
+    assert record["abs_path"] == "/workspace/_codex-worktrees/repo-main"
+
+
 def test_is_after_compares_tz_aware_iso():
     assert is_after("2026-05-25T19:25:00-07:00", "2026-05-17T05:01:39+00:00")
     assert not is_after("2026-05-10T00:00:00+00:00", "2026-05-17T05:01:39+00:00")
@@ -230,6 +315,7 @@ def test_prepare_pilot_builds_records_and_reports_missing_dirs(tmp_path):
 
     result = prepare_pilot(str(snap_path), per_tier={"full": 4})
 
+    assert result["state"] == "ready"
     assert result["workspace_root"] == str(workspace)
     assert len(result["records"]) == 1
     assert len(result["errors"]) == 1
@@ -244,3 +330,133 @@ def test_prepare_pilot_builds_records_and_reports_missing_dirs(tmp_path):
     assert record["drifted"] is False  # no git repo → not drifted
     assert result["errors"][0]["error"] == "missing_dir"
     assert result["errors"][0]["project_key"] == "GhostRepo"
+
+
+def test_prepare_pilot_blocks_unknown_checkout_authority(tmp_path):
+    workspace = tmp_path / "ws"
+    repo = workspace / "ConflictedRepo"
+    repo.mkdir(parents=True)
+    (repo / "AGENTS.md").write_text("# ConflictedRepo\n")
+    safe_repo = workspace / "SafeRepo"
+    safe_repo.mkdir()
+    (safe_repo / "AGENTS.md").write_text("# SafeRepo\n")
+    snapshot = {
+        "workspace_root": str(workspace),
+        "generated_at": "2026-08-03T12:00:00+00:00",
+        "projects": [
+            {
+                "identity": {
+                    "project_key": "ConflictedRepo",
+                    "path": "ConflictedRepo",
+                    "display_name": "ConflictedRepo",
+                },
+                "derived": {
+                    "archived": False,
+                    "context_quality": "full",
+                    "context_files": ["AGENTS.md"],
+                    "run_instructions_present": False,
+                },
+                "repository_state": {
+                    "checkout_authority": _checkout_authority(
+                        canonical_path="ConflictedRepo",
+                        state="unknown",
+                        reason_code=(
+                            "declared_path_conflicts_with_representative"
+                        ),
+                    )
+                },
+            },
+            {
+                "identity": {
+                    "project_key": "SafeRepo",
+                    "path": "SafeRepo",
+                    "display_name": "SafeRepo",
+                },
+                "derived": {
+                    "archived": False,
+                    "context_quality": "full",
+                    "context_files": ["AGENTS.md"],
+                    "run_instructions_present": False,
+                },
+            },
+        ],
+    }
+    snap_path = tmp_path / "snap.json"
+    snap_path.write_text(json.dumps(snapshot))
+
+    result = prepare_pilot(str(snap_path), per_tier={"full": 2})
+
+    assert result["state"] == "blocked"
+    assert result["records"] == []
+    assert result["errors"] == [
+        {
+            "project_key": "ConflictedRepo",
+            "abs_path": str(repo),
+            "error": "checkout_authority_blocked",
+            "reason": (
+                "checkout-authority-unknown:declared_path_conflicts_with_representative"
+            ),
+        }
+    ]
+
+
+def test_prepare_pilot_malformed_authority_never_redirects_error_path(tmp_path):
+    workspace = tmp_path / "ws"
+    repo = workspace / "CanonicalRepo"
+    repo.mkdir(parents=True)
+    (repo / "AGENTS.md").write_text("# CanonicalRepo\n")
+    base_project = {
+        "identity": {
+            "project_key": "CanonicalRepo",
+            "path": "CanonicalRepo",
+            "display_name": "CanonicalRepo",
+        },
+        "derived": {
+            "archived": False,
+            "context_quality": "full",
+            "context_files": ["AGENTS.md"],
+            "run_instructions_present": False,
+        },
+    }
+    variants = []
+
+    missing_field = _checkout_authority(canonical_path="CanonicalRepo")
+    missing_field.pop("origin")
+    variants.append(missing_field)
+
+    invalid_type = _checkout_authority(canonical_path="CanonicalRepo")
+    invalid_type["selection"] = "selected"
+    variants.append(invalid_type)
+
+    invalid_count = _checkout_authority(canonical_path="CanonicalRepo")
+    invalid_count["checkout_count"] = 3
+    variants.append(invalid_count)
+
+    malformed_record = _checkout_authority(canonical_path="CanonicalRepo")
+    del malformed_record["checkouts"][0]["head"]
+    variants.append(malformed_record)
+
+    snapshot = {
+        "workspace_root": str(workspace),
+        "generated_at": "2026-08-03T12:00:00+00:00",
+        "projects": [],
+    }
+    snap_path = tmp_path / "snap.json"
+    for authority in variants:
+        project = deepcopy(base_project)
+        project["repository_state"] = {"checkout_authority": authority}
+        snapshot["projects"] = [project]
+        snap_path.write_text(json.dumps(snapshot))
+
+        result = prepare_pilot(str(snap_path), per_tier={"full": 1})
+
+        assert result["state"] == "blocked"
+        assert result["records"] == []
+        assert result["errors"] == [
+            {
+                "project_key": "CanonicalRepo",
+                "abs_path": str(repo),
+                "error": "checkout_authority_blocked",
+                "reason": "checkout-authority-malformed",
+            }
+        ]