Clean up database split: remove bd.jsonl and issues.jsonl duplicates

- Removed stale bd.jsonl (old data before compaction)
- Removed stale issues.jsonl (old data before compaction)
- Added config.json to track canonical JSONL filename (beads.jsonl)
- Database now has single source of truth: beads.jsonl (167 issues)
- No code changes needed - FindJSONLPath() glob correctly finds existing beads.jsonl

Amp-Thread-ID: https://ampcode.com/threads/T-f25fe193-4185-40be-b5bc-e5725a3dbf1b
Co-authored-by: Amp <amp@ampcode.com>

.beads/beads.jsonl

@@ -72,6 +72,8 @@
 {"id":"bd-163","title":"Add .beads/config.json for database path configuration","description":"Create config file to eliminate ambiguity about which database is active.\n\nConfig file format (.beads/config.json):\n{\n  \"database\": \"beads.db\",\n  \"version\": \"0.17.5\",\n  \"jsonl_export\": \"beads.jsonl\"  // Allow user to rename\n}\n\nImplementation:\n- bd init creates config.json\n- Daemon and clients read config first (single source of truth)\n- Fall back to beads.db if config missing (backward compat)\n- bd init --jsonl-name allows customizing export filename\n- Gitignore: do NOT ignore config.json (part of repo state)\n\nBenefits:\n- Explicit configuration over convention\n- Allows JSONL renaming for git history hygiene\n- Single source of truth for file paths","status":"closed","priority":2,"issue_type":"task","created_at":"2025-10-26T18:06:07.571909-07:00","updated_at":"2025-10-26T18:44:16.133085-07:00","closed_at":"2025-10-26T18:44:16.133085-07:00","dependencies":[{"issue_id":"bd-163","depends_on_id":"bd-159","type":"parent-child","created_at":"2025-10-26T18:06:07.572636-07:00","created_by":"daemon"}]}
 {"id":"bd-164","title":"Add migration tooling for database upgrades","description":"Create bd migrate command and auto-migration logic for version upgrades.\n\nImplementation:\n- bd migrate command (or bd init --migrate)\n- Auto-run on first command after daemon version upgrade\n- Detection logic:\n  - Find all .db files in .beads/\n  - Check schema version in each\n  - Prompt to migrate/rename/delete\n- Migration operations:\n  - Rename old database to beads.db\n  - Update schema version metadata\n  - Remove stale databases (with confirmation)\n- Could be part of daemon auto-start logic\n\nUser experience:\n$ bd ready\nDatabase schema mismatch detected.\n  Found: vc.db (schema v0.16.0)\n  Expected: beads.db (schema v0.17.5)\n  \nRun 'bd migrate' to migrate automatically.\n\nBenefits:\n- Smooth upgrade path\n- Prevents confusion on version changes\n- Clean up stale databases\n\nDepends on:\n- Canonical naming (bd-160)\n- Schema versioning (bd-161)","status":"closed","priority":2,"issue_type":"task","created_at":"2025-10-26T18:06:07.571855-07:00","updated_at":"2025-10-26T19:04:02.023089-07:00","closed_at":"2025-10-26T19:04:02.023089-07:00","dependencies":[{"issue_id":"bd-164","depends_on_id":"bd-159","type":"parent-child","created_at":"2025-10-26T18:06:07.573546-07:00","created_by":"daemon"},{"issue_id":"bd-164","depends_on_id":"bd-162","type":"blocks","created_at":"2025-10-26T18:06:17.327717-07:00","created_by":"daemon"},{"issue_id":"bd-164","depends_on_id":"bd-160","type":"blocks","created_at":"2025-10-26T18:06:17.351768-07:00","created_by":"daemon"}]}
 {"id":"bd-165","title":"Enforce canonical database name (beads.db)","description":"Always use beads.db as the canonical database name. Never auto-detect from multiple .db files.\n\nImplementation:\n- bd init always creates/uses beads.db\n- bd init detects and migrates old databases (vc.db → beads.db, bd.db → beads.db)\n- Daemon refuses to start if multiple .db files exist in .beads/ (exit with ambiguity error)\n- Update database discovery logic to prefer beads.db, error on ambiguity\n\nBenefits:\n- Prevents accidental use of stale databases\n- Clear single source of truth\n- Migration path for existing users","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-26T18:06:18.33827-07:00","updated_at":"2025-10-26T18:10:34.132537-07:00","closed_at":"2025-10-26T18:10:34.132537-07:00","dependencies":[{"issue_id":"bd-165","depends_on_id":"bd-159","type":"parent-child","created_at":"2025-10-26T18:06:18.339465-07:00","created_by":"daemon"}]}
+{"id":"bd-166","title":"Test database naming","description":"","status":"open","priority":2,"issue_type":"task","created_at":"2025-10-27T18:10:47.11308-07:00","updated_at":"2025-10-27T18:10:47.11308-07:00"}
+{"id":"bd-167","title":"Final validation test","description":"","status":"open","priority":2,"issue_type":"task","created_at":"2025-10-27T18:19:58.016545-07:00","updated_at":"2025-10-27T18:19:58.016545-07:00"}
 {"id":"bd-17","title":"Update EXTENDING.md with UnderlyingDB() usage and best practices","description":"EXTENDING.md currently shows how to use direct sql.Open() to access the database, but doesn't mention the new UnderlyingDB() method that's the recommended way for extensions.\n\n**Update needed:**\n1. Add section showing UnderlyingDB() usage:\n   ```go\n   store, err := beads.NewSQLiteStorage(dbPath)\n   db := store.UnderlyingDB()\n   // Create extension tables using db\n   ```\n\n2. Document when to use UnderlyingDB() vs direct sql.Open():\n   - Use UnderlyingDB() when you want to share the storage connection\n   - Use sql.Open() when you need independent connection management\n\n3. Add safety warnings (cross-reference from UnderlyingDB() docs):\n   - Don't close the DB\n   - Don't modify pool settings\n   - Keep transactions short\n\n4. Update the VC example to show UnderlyingDB() pattern\n\n5. Explain beads.Storage.UnderlyingDB() in the API section","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-22T17:07:56.820056-07:00","updated_at":"2025-10-25T23:15:33.478579-07:00","closed_at":"2025-10-22T19:41:19.895847-07:00","dependencies":[{"issue_id":"bd-17","depends_on_id":"bd-10","type":"discovered-from","created_at":"2025-10-24T13:17:40.32522-07:00","created_by":"renumber"}]}
 {"id":"bd-18","title":"Consider adding UnderlyingConn(ctx) for safer scoped DB access","description":"Currently UnderlyingDB() returns *sql.DB which is correct for most uses, but for extension migrations/DDL, a scoped connection might be safer.\n\n**Proposal:** Add optional UnderlyingConn(ctx) (*sql.Conn, error) method that:\n- Returns a scoped connection via s.db.Conn(ctx)\n- Encourages lifetime-bounded usage\n- Reduces temptation to tune global pool settings\n- Better for one-time DDL operations like CREATE TABLE\n\n**Implementation:**\n```go\n// UnderlyingConn returns a single connection from the pool for scoped use\n// Useful for migrations and DDL. Close the connection when done.\nfunc (s *SQLiteStorage) UnderlyingConn(ctx context.Context) (*sql.Conn, error) {\n    return s.db.Conn(ctx)\n}\n```\n\n**Benefits:**\n- Safer for migrations (explicit scope)\n- Complements UnderlyingDB() for different use cases\n- Low implementation cost\n\n**Trade-off:** Adds another method to maintain, but Oracle considers this balanced compromise between safety and flexibility.\n\n**Decision:** This is optional - evaluate based on VC's actual usage patterns.","status":"closed","priority":3,"issue_type":"feature","created_at":"2025-10-22T17:07:56.832638-07:00","updated_at":"2025-10-25T23:15:33.479496-07:00","closed_at":"2025-10-22T22:02:18.479512-07:00","dependencies":[{"issue_id":"bd-18","depends_on_id":"bd-10","type":"related","created_at":"2025-10-24T13:17:40.325463-07:00","created_by":"renumber"}]}
 {"id":"bd-19","title":"MCP close tool method signature error - takes 1 positional argument but 2 were given","description":"The close approval routing fix in beads-mcp v0.11.0 works correctly and successfully routes update(status=\"closed\") calls to close() tool. However, the close() tool has a Python method signature bug that prevents execution.\n\nImpact: All MCP-based close operations are broken. Workaround: Use bd CLI directly.\n\nError: BdDaemonClient.close() takes 1 positional argument but 2 were given\n\nRoot cause: BdDaemonClient.close() only accepts self, but MCP tool passes issue_id and reason.\n\nAdditional issue: CLI close has FOREIGN KEY constraint error when recording reason parameter.\n\nSee GitHub issue #107 for full details.","status":"closed","priority":0,"issue_type":"bug","created_at":"2025-10-22T17:25:34.67056-07:00","updated_at":"2025-10-25T23:15:33.480292-07:00","closed_at":"2025-10-22T17:36:55.463445-07:00"}

.beads/config.json

@@ -0,0 +1,5 @@
+{
+  "database": "beads.db",
+  "version": "0.17.7",
+  "jsonl_export": "beads.jsonl"
+}