fix(core): context engineering post-review fixes (#229, #230, #231, #232)

[bug-ops]

Summary

Post-implementation review of v0.9.4 context engineering identified 5 gaps. This PR fixes the top 4 (P0-P2):

• Persist message parts to SQLite #229 (P0): Wire persist_message() to call remember_with_parts(), persisting MessagePart data to SQLite instead of always writing empty []
• Free pruned tool output bodies from memory #230 (P1): Clear tool output body string after marking as compacted in prune_tool_outputs() to reclaim heap memory
• Cache repo map with TTL to avoid per-message regeneration #231 (P1): Cache generate_repo_map() result with configurable TTL (default 300s) to avoid per-message filesystem traversal
• Add score threshold to cross-session memory search #232 (P2): Filter cross-session memory search results by score threshold (default 0.35) to reduce noise in context

Gap 5 (#233, file watcher for code index) deferred to follow-up PR.

Test plan

• Existing test suite passes (1276 tests, 0 failures)
• New test: remember_with_parts_saves_parts_json — verifies parts JSON persisted to SQLite
• Updated test: test_prune_frees_tokens — asserts body is empty after prune
• New test: test_repo_map_cache_hit — validates cache field populated and stable
• New test: test_cross_session_score_threshold_filters — verifies score filtering

Closes #229, closes #230, closes #231, closes #232

[codecov-commenter]

Codecov Report

❌ Patch coverage is 64.86486% with 52 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
crates/zeph-core/src/agent.rs	64.13%	33 Missing ⚠️
crates/zeph-memory/src/semantic.rs	61.70%	18 Missing ⚠️
src/main.rs	0.00%	1 Missing ⚠️

@@            Coverage Diff             @@
##             main     #235      +/-   ##
==========================================
- Coverage   81.04%   80.96%   -0.08%     
==========================================
  Files          78       78              
  Lines       22999    23137     +138     
==========================================
+ Hits        18640    18734      +94     
- Misses       4359     4403      +44     

Files with missing lines	Coverage Δ
crates/zeph-core/src/config.rs	98.92% <100.00%> (+<0.01%)	⬆️
src/main.rs	70.85% <0.00%> (-0.06%)	⬇️
crates/zeph-memory/src/semantic.rs	78.95% <61.70%> (-0.97%)	⬇️
crates/zeph-core/src/agent.rs	69.17% <64.13%> (+<0.01%)	⬆️

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