fix(sqlite): move the non-daemon stores off WAL to rollback journalling (#356)

src/pinky_daemon/activity_store.py

@@ -13,6 +13,8 @@
 import time
 from pathlib import Path
 
+from pinky_daemon.sqlite_journal import configure_rollback_journal
+
 
 class ActivityStore:
     """SQLite-backed activity log."""
@@ -29,8 +31,7 @@ def _db(self) -> sqlite3.Connection:
         connection = getattr(self._thread_local, "connection", None)
         if connection is None:
             connection = sqlite3.connect(self._db_path)
-            connection.execute("PRAGMA journal_mode=WAL")
-            connection.execute("PRAGMA busy_timeout=30000")
+            configure_rollback_journal(connection, db_label="activity.db")
             self._thread_local.connection = connection
         return connection
 

src/pinky_daemon/agent_comms.py

@@ -23,6 +23,8 @@
 from dataclasses import dataclass, field
 from pathlib import Path
 
+from pinky_daemon.sqlite_journal import configure_rollback_journal
+
 
 @dataclass
 class AgentMessage:
@@ -83,8 +85,7 @@ def _conn(self) -> sqlite3.Connection:
         if connection is None:
             connection = sqlite3.connect(self._db_path)
             connection.row_factory = sqlite3.Row
-            connection.execute("PRAGMA journal_mode=WAL")
-            connection.execute("PRAGMA busy_timeout=30000")
+            configure_rollback_journal(connection, db_label="agent_comms.db")
             self._thread_local.connection = connection
         return connection
 

src/pinky_daemon/analytics_store.py

@@ -6,6 +6,8 @@
 from contextlib import contextmanager
 from datetime import UTC, datetime, timedelta
 
+from pinky_daemon.sqlite_journal import configure_rollback_journal
+
 # Providers to include in analytics dashboards.
 # Only Anthropic/Claude usage — excludes Codex CLI (OpenAI) and other non-Anthropic providers.
 _ANTHROPIC_PROVIDERS = {"firstParty", "default", "anthropic", "bedrock", "vertex"}
@@ -77,10 +79,12 @@ def _connect(self):
 
     def _init_db(self) -> None:
         with self._connect() as conn:
+            # Runs once per store construction, before any other connection is
+            # handed out. TRUNCATE is persisted in the database header, so the
+            # short-lived connections from _connect() inherit it.
+            configure_rollback_journal(conn, db_label="analytics.db")
             conn.executescript(
                 """
-                PRAGMA journal_mode=WAL;
-
                 CREATE TABLE IF NOT EXISTS analytics_session_facts (
                   session_id TEXT PRIMARY KEY,
                   agent_name TEXT NOT NULL,

src/pinky_daemon/app_store.py

@@ -18,6 +18,8 @@
 from dataclasses import dataclass
 from pathlib import Path
 
+from pinky_daemon.sqlite_journal import configure_rollback_journal
+
 
 def _log(msg: str) -> None:
     print(msg, file=sys.stderr, flush=True)
@@ -78,7 +80,7 @@ def __init__(self, db_path: str = "data/apps.db") -> None:
         Path(db_path).parent.mkdir(parents=True, exist_ok=True)
         self._db_path = db_path
         self._db = sqlite3.connect(db_path, check_same_thread=False)
-        self._db.execute("PRAGMA journal_mode=WAL")
+        configure_rollback_journal(self._db, db_label="apps.db")
         self._db.execute("PRAGMA foreign_keys=ON")
         self._init_tables()
 

src/pinky_daemon/conversation_store.py

@@ -18,6 +18,8 @@
 from dataclasses import dataclass, field
 from pathlib import Path
 
+from pinky_daemon.sqlite_journal import configure_rollback_journal
+
 
 def _fts5_phrase(query: str) -> str:
     """Escape a user query as quoted FTS5 phrase tokens (no operator syntax)."""
@@ -94,8 +96,7 @@ def _conn(self) -> sqlite3.Connection:
         if connection is None:
             connection = sqlite3.connect(self._db_path)
             connection.row_factory = sqlite3.Row
-            connection.execute("PRAGMA journal_mode=WAL")
-            connection.execute("PRAGMA busy_timeout=30000")
+            configure_rollback_journal(connection, db_label="conversations.db")
             self._thread_local.connection = connection
         return connection
 

src/pinky_daemon/dream_runner.py

@@ -33,6 +33,7 @@
 )
 from pinky_daemon.dream_prompt import DREAM_SYSTEM_PROMPT
 from pinky_daemon.sdk_runner import SDKRunner, SDKRunnerConfig
+from pinky_daemon.sqlite_journal import configure_rollback_journal
 from pinky_daemon.tmux_dream_runner import TmuxDreamConfig, TmuxDreamRunner
 
 
@@ -114,8 +115,7 @@ def _db(self) -> sqlite3.Connection:
         connection = getattr(self._thread_local, "connection", None)
         if connection is None:
             connection = sqlite3.connect(self._db_path)
-            connection.execute("PRAGMA journal_mode=WAL")
-            connection.execute("PRAGMA busy_timeout=30000")
+            configure_rollback_journal(connection, db_label="dreams.db")
             self._thread_local.connection = connection
         return connection
 

src/pinky_daemon/hooks.py

@@ -23,6 +23,8 @@
 from enum import Enum
 from pathlib import Path
 
+from pinky_daemon.sqlite_journal import configure_rollback_journal
+
 
 def _log(msg: str) -> None:
     print(msg, file=sys.stderr, flush=True)
@@ -133,8 +135,7 @@ def _db(self) -> sqlite3.Connection:
         connection = getattr(self._thread_local, "connection", None)
         if connection is None:
             connection = sqlite3.connect(self._db_path)
-            connection.execute("PRAGMA journal_mode=WAL")
-            connection.execute("PRAGMA busy_timeout=30000")
+            configure_rollback_journal(connection, db_label="audit.db")
             self._thread_local.connection = connection
         return connection
 

src/pinky_daemon/kb_store.py

@@ -34,6 +34,8 @@
 
 import yaml
 
+from pinky_daemon.sqlite_journal import configure_rollback_journal
+
 
 def _log(msg: str) -> None:
     print(msg, file=sys.stderr, flush=True)
@@ -177,7 +179,7 @@ def __init__(self, data_dir: str | Path) -> None:
 
     def _conn(self) -> sqlite3.Connection:
         conn = sqlite3.connect(str(self.db_path))
-        conn.execute("PRAGMA journal_mode=WAL")
+        configure_rollback_journal(conn, db_label="kb.db")
         conn.execute("PRAGMA foreign_keys=ON")
         conn.row_factory = sqlite3.Row
         return conn

src/pinky_daemon/librarian_runner.py

@@ -22,6 +22,7 @@
 from pinky_daemon.kb_store import _FRONTMATTER_RE, KBStore, _content_hash
 from pinky_daemon.librarian_prompt import LIBRARIAN_SYSTEM_PROMPT
 from pinky_daemon.sdk_runner import SDKRunner, SDKRunnerConfig
+from pinky_daemon.sqlite_journal import configure_rollback_journal
 
 
 def _log(msg: str) -> None:
@@ -66,7 +67,7 @@ def __init__(
 
     def _conn(self) -> sqlite3.Connection:
         conn = sqlite3.connect(str(self._db_path))
-        conn.execute("PRAGMA journal_mode=WAL")
+        configure_rollback_journal(conn, db_label="librarian_state.db")
         conn.row_factory = sqlite3.Row
         return conn
 

src/pinky_daemon/mesh_store.py

@@ -29,6 +29,8 @@
 from pathlib import Path
 from typing import Any, Literal
 
+from pinky_daemon.sqlite_journal import configure_rollback_journal
+
 # -- Records -------------------------------------------------------------------
 
 
@@ -102,7 +104,7 @@ class MeshStore:
     def __init__(self, db_path: str = "data/mesh.db") -> None:
         Path(db_path).parent.mkdir(parents=True, exist_ok=True)
         self._db = sqlite3.connect(db_path, check_same_thread=False)
-        self._db.execute("PRAGMA journal_mode=WAL")
+        configure_rollback_journal(self._db, db_label="mesh.db")
         self._db.execute("PRAGMA foreign_keys=ON")
         self._lock = threading.RLock()
         self._init_tables()

src/pinky_daemon/message_context_store.py

@@ -9,6 +9,8 @@
 from pathlib import Path
 from typing import Any
 
+from pinky_daemon.sqlite_journal import configure_rollback_journal
+
 DEFAULT_RETENTION_DAYS = 30
 DEFAULT_MAX_PER_AGENT = 1000
 
@@ -30,8 +32,10 @@ def __init__(
         Path(db_path).parent.mkdir(parents=True, exist_ok=True)
         self._db = sqlite3.connect(db_path, check_same_thread=False)
         self._db.row_factory = sqlite3.Row
-        self._db.execute("PRAGMA journal_mode=WAL")
-        self._db.execute("PRAGMA busy_timeout=5000")
+        # configure_rollback_journal also installs a 30s busy_timeout, which
+        # replaces the 5s this store used to set: rollback journalling
+        # serialises readers against the writer, so waiting longer is right.
+        configure_rollback_journal(self._db, db_label="message_context.db")
         self._create_schema()
         self._ensure_columns()
         self._ensure_identity_key()

src/pinky_daemon/outreach_config.py

@@ -17,6 +17,8 @@
 from dataclasses import dataclass, field
 from pathlib import Path
 
+from pinky_daemon.sqlite_journal import configure_rollback_journal
+
 
 def _log(msg: str) -> None:
     print(msg, file=sys.stderr, flush=True)
@@ -53,7 +55,7 @@ class OutreachConfigStore:
     def __init__(self, db_path: str = "data/outreach_config.db") -> None:
         Path(db_path).parent.mkdir(parents=True, exist_ok=True)
         self._db = sqlite3.connect(db_path, check_same_thread=False)
-        self._db.execute("PRAGMA journal_mode=WAL")
+        configure_rollback_journal(self._db, db_label="outreach_config.db")
         self._init_tables()
 
     def _init_tables(self) -> None:

src/pinky_daemon/plugin_manager.py

@@ -38,6 +38,8 @@
 
 import yaml
 
+from pinky_daemon.sqlite_journal import configure_rollback_journal
+
 
 def _log(msg: str) -> None:
     print(msg, file=sys.stderr, flush=True)
@@ -139,7 +141,7 @@ def db(self) -> sqlite3.Connection:
                 data_dir.mkdir(parents=True, exist_ok=True)
                 self._db_path = str(data_dir / "plugins.db")
             self._db = sqlite3.connect(self._db_path, check_same_thread=False)
-            self._db.execute("PRAGMA journal_mode=WAL")
+            configure_rollback_journal(self._db, db_label="plugins.db")
         return self._db
 
     def create_table(self, table_name: str, schema: str) -> None:
@@ -296,7 +298,7 @@ def _init_state_db(self) -> None:
         """Initialize the plugin state tracking table."""
         Path(self._state_db_path).parent.mkdir(parents=True, exist_ok=True)
         db = sqlite3.connect(self._state_db_path, check_same_thread=False)
-        db.execute("PRAGMA journal_mode=WAL")
+        configure_rollback_journal(db, db_label="plugins.db")
         db.execute("""
             CREATE TABLE IF NOT EXISTS plugin_state (
                 name TEXT PRIMARY KEY,

src/pinky_daemon/presentation_store.py

@@ -23,6 +23,8 @@
 from dataclasses import dataclass
 from pathlib import Path
 
+from pinky_daemon.sqlite_journal import configure_rollback_journal
+
 
 def _log(msg: str) -> None:
     print(msg, file=sys.stderr, flush=True)
@@ -137,8 +139,7 @@ def _db(self) -> sqlite3.Connection:
         connection = getattr(self._thread_local, "connection", None)
         if connection is None:
             connection = sqlite3.connect(self._db_path)
-            connection.execute("PRAGMA journal_mode=WAL")
-            connection.execute("PRAGMA busy_timeout=30000")
+            configure_rollback_journal(connection, db_label="presentations.db")
             connection.execute("PRAGMA foreign_keys=ON")
             self._thread_local.connection = connection
         return connection

src/pinky_daemon/research_store.py

@@ -23,6 +23,8 @@
 from dataclasses import dataclass, field
 from pathlib import Path
 
+from pinky_daemon.sqlite_journal import configure_rollback_journal
+
 
 def _log(msg: str) -> None:
     print(msg, file=sys.stderr, flush=True)
@@ -147,8 +149,7 @@ def _db(self) -> sqlite3.Connection:
         connection = getattr(self._thread_local, "connection", None)
         if connection is None:
             connection = sqlite3.connect(self._db_path)
-            connection.execute("PRAGMA journal_mode=WAL")
-            connection.execute("PRAGMA busy_timeout=30000")
+            configure_rollback_journal(connection, db_label="research.db")
             connection.execute("PRAGMA foreign_keys=ON")
             self._thread_local.connection = connection
         return connection

src/pinky_daemon/session_store.py

@@ -20,6 +20,8 @@
 from dataclasses import dataclass, field
 from pathlib import Path
 
+from pinky_daemon.sqlite_journal import configure_rollback_journal
+
 
 def _log(msg: str) -> None:
     print(msg, file=sys.stderr, flush=True)
@@ -71,8 +73,7 @@ def _db(self) -> sqlite3.Connection:
         connection = getattr(self._thread_local, "connection", None)
         if connection is None:
             connection = sqlite3.connect(self._db_path)
-            connection.execute("PRAGMA journal_mode=WAL")
-            connection.execute("PRAGMA busy_timeout=30000")
+            configure_rollback_journal(connection, db_label="sessions.db")
             self._thread_local.connection = connection
         return connection
 
@@ -314,8 +315,7 @@ def _db(self) -> sqlite3.Connection:
         connection = getattr(self._thread_local, "connection", None)
         if connection is None:
             connection = sqlite3.connect(self._db_path)
-            connection.execute("PRAGMA journal_mode=WAL")
-            connection.execute("PRAGMA busy_timeout=30000")
+            configure_rollback_journal(connection, db_label="sessions.db")
             self._thread_local.connection = connection
         return connection
 

src/pinky_daemon/skill_store.py

@@ -29,6 +29,8 @@
 from enum import Enum
 from pathlib import Path
 
+from pinky_daemon.sqlite_journal import configure_rollback_journal
+
 
 def _log(msg: str) -> None:
     print(msg, file=sys.stderr, flush=True)
@@ -153,8 +155,7 @@ def _db(self) -> sqlite3.Connection:
         connection = getattr(self._thread_local, "connection", None)
         if connection is None:
             connection = sqlite3.connect(self._db_path)
-            connection.execute("PRAGMA journal_mode=WAL")
-            connection.execute("PRAGMA busy_timeout=30000")
+            configure_rollback_journal(connection, db_label="skills.db")
             connection.execute("PRAGMA foreign_keys=ON")
             self._thread_local.connection = connection
         return connection