Implement multi-repo hydration layer with mtime caching (bd-307)

- Add repo_mtimes table to track JSONL file modification times
- Implement HydrateFromMultiRepo() with mtime-based skip optimization
- Support tilde expansion for repo paths in config
- Add source_repo column via migration (not in base schema)
- Fix schema to allow migration on existing databases
- Comprehensive test coverage for hydration logic
- Resurrect missing parent issues bd-cb64c226 and bd-cbed9619

Implementation:
- internal/storage/sqlite/multirepo.go - Core hydration logic
- internal/storage/sqlite/multirepo_test.go - Test coverage
- docs/MULTI_REPO_HYDRATION.md - Documentation

Schema changes:
- source_repo column added via migration only (not base schema)
- repo_mtimes table for mtime caching
- All SELECT queries updated to include source_repo

Database recovery:
- Restored from 17 to 285 issues
- Created placeholder parents for orphaned hierarchical children

Amp-Thread-ID: https://ampcode.com/threads/T-faa1339a-14b2-426c-8e18-aa8be6f5cde6
Co-authored-by: Amp <amp@ampcode.com>

internal/storage/sqlite/schema.go

@@ -166,6 +166,17 @@ CREATE TABLE IF NOT EXISTS compaction_snapshots (
 
 CREATE INDEX IF NOT EXISTS idx_comp_snap_issue_level_created ON compaction_snapshots(issue_id, compaction_level, created_at DESC);
 
+-- Repository mtimes table (for multi-repo hydration optimization)
+-- Tracks modification times of JSONL files to skip unchanged repos
+CREATE TABLE IF NOT EXISTS repo_mtimes (
+    repo_path TEXT PRIMARY KEY,  -- Absolute path to the repository root
+    jsonl_path TEXT NOT NULL,    -- Absolute path to the .beads/issues.jsonl file
+    mtime_ns INTEGER NOT NULL,   -- Modification time in nanoseconds since epoch
+    last_checked DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP
+);
+
+CREATE INDEX IF NOT EXISTS idx_repo_mtimes_checked ON repo_mtimes(last_checked);
+
 -- Ready work view (with hierarchical blocking)
 -- Uses recursive CTE to propagate blocking through parent-child hierarchy
 CREATE VIEW IF NOT EXISTS ready_issues AS