#12766: fix(memory): bootstrap session indexing on cold start

## Problem Two related bugs prevent session memory from working correctly: ### 1. Cold-start deadlock in `shouldSyncSessions()` (src/memory/manager.ts) After a restart, `sessionsDirty` is `false` and `sessionsDirtyFiles` is empty (both are only set by runtime delta events). If `needsFullReindex` is also `false` (DB exists with valid fingerprint), the method always returns `false` and session files are never indexed. **Observed:** 115 session files on disk, only 53 indexed. The 62 missing files are permanently invisible. ### 2. `extraDirs` hooks overridden by bundled hooks (src/hooks/workspace.ts) The hook merge order places `extraDirs` *before* bundled hooks: ``` extra → bundled → managed → workspace ``` Since later entries overwrite earlier ones in the Map, bundled hooks always win over `extraDirs` with the same name. This makes it impossible to patch a bundled hook (e.g. `session-memory`) via `extraDirs`. ## Fixes ### Commit 1: `fix(memory): bootstrap session indexing on cold start` - Add a one-time cold-start check in `shouldSyncSessions()` comparing indexed session rows vs files on disk - When files outnumber indexed rows, force a catch-up sync - Check runs at most once per manager lifetime (cached in `sessionsColdStartNeeded`) - Uses sync `readdirSync` to stay cheap - Logs `sessions cold-start: N files on disk, M indexed — will sync` for observability ### Commit 2: `fix(hooks): extraDirs should override bundled hooks, not the reverse` - Swap merge order: bundled loads first, then `extraDirs` overwrites - Managed and workspace hooks still take highest priority - One-line change + comment update ## Scope 2 files changed: `src/memory/manager.ts` (+40 lines), `src/hooks/workspace.ts` (+3/-2 lines) ## Not addressed (future work) - Bounded/chunked bootstrap sync for very large session directories (timeout mitigation) - `--verbose` skip-reason logging for `shouldSyncSessions` Ref: #12633