1. Timeline sort: ContentStore results get timestamp fallback (new Date())
2. Read path no longer mutates state: knowledge-reuse write removed from
   ctx_search (read tool should not write)
3. configDir: use CLAUDE_CONFIG_DIR env var + absolute path (fixes #290 regression)
4. SessionDB: open once before query loop, close in finally (was per-query)
5. Auto-memory: 1MB file size guard on readFileSync
6. Debug logging: all catch blocks log with DEBUG=context-mode env var

Removes 3 knowledge-reuse tests that validated deleted write-on-read behavior.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* feat: unified persistent memory & timeline search (#363)

Two pillars for session continuity after compaction:

Pillar 1 — Unified Timeline Search:
- ctx_search gains sort="timeline" mode searching 3 sources chronologically
- ContentStore (current session) + SessionDB (prior sessions) + auto-memory
- Default sort="relevance" preserves current behavior exactly
- New searchAllSources() in src/search/unified.ts
- SessionDB.searchEvents() with project_dir filter + LIKE escaping
- searchAutoMemory() with adapter-aware dash-separated paths
- FTS5 schema migration: 4 new UNINDEXED columns (source_category, session_id, event_id, timestamp)

Pillar 2 — Auto-Injection on Compaction:
- buildAutoInjection() fires ONLY on SessionStart(source="compact")
- <behavioral_directive> for roles, <rules> for decisions, <active_skills> for skills
- 500 token hard cap with priority-based overflow strategy
- Never fires mid-session — context-mode does not pollute the context it protects

Static Reinforcement (~99 tokens, session start only):
- 12 adapter configs: Session Continuity + MEMORY sections (4 tiers by hook support)
- routing-block.mjs: <session_continuity> tag + tool hierarchy 0. MEMORY
- ctx_search tool description: SESSION STATE reminder

Bug Fixes:
- snapshot.ts: add missing case "role" + buildRolesSection()
- extract.ts: skill priority P3 → P2
- pi-extension.ts: minPriority 2 → 3

12 New Categories:
Phase 1: user-prompt, compaction, rejected-approach, session-resume, constraint, knowledge-reuse
Phase 2: agent-finding, error-resolution, external-ref, blocked-on, iteration-loop, latency

8 review rounds, 16+ engineers per round, TDD-first implementation.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: move rejected-approach from pretooluse to posttooluse via marker file

PreToolUse cannot safely load SessionDB (native module loading breaks
hook stdout on CI). Use tmpdir marker file pattern (same as latency)
instead: pretooluse writes marker, posttooluse reads and writes event.

Also implements knowledge-reuse event (search_hit_prior) with sessionId
wiring and 3 new tests.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: wire searchAllSources into ctx_search handler + skip empty guard for timeline

Two critical wiring bugs found by final review:
1. searchAllSources was imported but never called — sort="timeline" silently
   fell back to ContentStore-only search
2. Empty-index guard blocked timeline mode even when SessionDB had data

Now sort="timeline" creates a read-only SessionDB connection and calls
searchAllSources() for unified 3-source search. Default sort="relevance"
unchanged — calls store.searchWithFallback() directly.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: correct tool name prefixes in qwen-code, openclaw, kilo adapter configs

- qwen-code: bare ctx_* → mcp__context-mode__ctx_* (22 refs)
- openclaw: bare ctx_search → context-mode__ctx_search (line 49)
- kilo: bare ctx_search → context-mode_ctx_search (line 49)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: address PR review — 6 blockers resolved

1. Timeline sort: ContentStore results get timestamp fallback (new Date())
2. Read path no longer mutates state: knowledge-reuse write removed from
   ctx_search (read tool should not write)
3. configDir: use CLAUDE_CONFIG_DIR env var + absolute path (fixes #290 regression)
4. SessionDB: open once before query loop, close in finally (was per-query)
5. Auto-memory: 1MB file size guard on readFileSync
6. Debug logging: all catch blocks log with DEBUG=context-mode env var

Removes 3 knowledge-reuse tests that validated deleted write-on-read behavior.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: timeline timestamp correctness + output format + CI fix

1. auto-memory: set timestamp from file mtime (was missing entirely)
2. ContentStore: use sessionStartTime instead of new Date() per-result
3. Normalize SQLite datetime format to ISO before sort
4. Output headers show origin + timestamp: [prior-session | 2026-04-27 14:30 | source]
5. pretooluse.mjs: move marker writes BEFORE stdout (fixes macOS CI timeout)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: macOS CI + auto-memory match quality + snippet boundaries

1. macOS CI: test sentinel path uses /tmp (matching sentinelDir()) instead
   of tmpdir() which returns /var/folders/... on macOS — fixes isMCPReady()
   returning false in CI, causing all redirect assertions to fail
2. Auto-memory: raise minimum term length from 2 to 3 chars, use word
   boundary regex instead of String.includes() (prevents "if" matching
   "specific", "definition", etc.)
3. Snippet extraction: walk to nearest paragraph boundary (\n\n) instead
   of cutting mid-word at arbitrary byte offset

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* fix: surface real timestamps from FTS5 chunks for correct timeline sort

ContentStore search results now carry actual indexing timestamps instead
of falling back to Date.now(). Changes:

1. store.ts: add chunks.timestamp to all 12 search SQL SELECT statements
2. store.ts: populate timestamp on INSERT with new Date().toISOString()
3. types.ts: add timestamp to SearchResult interface
4. unified.ts: use r.timestamp from ContentStore, fallback sessionStartTime

Timeline sort now produces correct chronological ordering across all 3
sources (ContentStore indexed_at, SessionDB created_at, auto-memory mtime).

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* chore: remove session bundle files from PR

Session bundles (session-db, session-extract, session-snapshot) are
CI-generated artifacts. Only server.bundle.mjs and cli.bundle.mjs
belong in commits. CI will regenerate session bundles on merge.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

* chore: remove PRD from PR — belongs in issues, not in repo

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

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Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>