Fix MCP close method signature bug (GH #107, bd-67)

- Fix BdDaemonClient.close() to accept issue_id and reason parameters
- Remove uv.lock from repo

Amp-Thread-ID: https://ampcode.com/threads/T-0017f48d-605c-410f-9a77-db62153c9357
Co-authored-by: Amp <amp@ampcode.com>

.beads/beads.jsonl

@@ -63,6 +63,7 @@
 {"id":"bd-66","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":"open","priority":3,"issue_type":"feature","created_at":"2025-10-22T17:07:56.832638-07:00","updated_at":"2025-10-22T17:07:56.832638-07:00","dependencies":[{"issue_id":"bd-66","depends_on_id":"bd-57","type":"related","created_at":"2025-10-22T17:07:56.835844-07:00","created_by":"daemon"}]}
 {"id":"bd-67","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":"2025-10-22T17:36:55.463445-07:00","closed_at":"2025-10-22T17:36:55.463445-07:00"}
 {"id":"bd-68","title":"Test close issue","description":"","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-22T17:27:56.89475-07:00","updated_at":"2025-10-22T17:28:00.795511-07:00","closed_at":"2025-10-22T17:28:00.795511-07:00"}
+{"id":"bd-69","title":"Fix pre-existing MCP test failures - show/update return arrays not dicts","description":"9 tests fail in beads-mcp because bd CLI commands return arrays but MCP client expects dicts:\n\nFailing tests:\n- test_create_and_show_issue: show returns array, expects dict\n- test_update_issue: update returns array, expects dict  \n- test_add_dependency: show returns array, expects dict\n- test_invalid_issue_id: show returns empty dict instead of error\n- test_dependency_types: show returns array, expects dict\n- test_show_issue_tool: show returns array, expects dict\n- test_update_issue_tool: update returns array, expects dict\n- test_update_partial_fields: update returns array, expects dict\n- test_client_lazy_initialization: BdClient import issue\n\nRoot cause: bd CLI commands like 'bd show' and 'bd update' output JSON arrays, but BdCliClient.show() and BdCliClient.update() expect single dict objects.\n\nExample:\n```bash\nbd show test-1 --json\n[{\"id\":\"test-1\",...}]  # Array, not dict\n```\n\nFix needed: Update bd_client.py to handle array responses and extract first element, or change CLI to return single object for single-ID operations.","status":"in_progress","priority":1,"issue_type":"bug","created_at":"2025-10-22T17:43:23.29302-07:00","updated_at":"2025-10-22T17:47:06.900031-07:00"}
 {"id":"bd-7","title":"Write tests for merge functionality","description":"Unit tests: validation, merge logic, data integrity. Integration tests: end-to-end workflow, export/import. Edge case tests: chains, circular refs, epics.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-21T23:53:44.31362-07:00","updated_at":"2025-10-22T11:56:36.523309-07:00","closed_at":"2025-10-22T01:07:04.72062-07:00"}
 {"id":"bd-8","title":"Improve error handling in dependency removal during remapping","description":"In updateDependencyReferences(), RemoveDependency errors are caught and ignored with continue (line 392). Comment says 'if dependency doesn't exist' but this catches ALL errors including real failures. Should check error type with errors.Is(err, ErrDependencyNotFound) and only ignore not-found errors, returning other errors properly.","status":"closed","priority":3,"issue_type":"bug","created_at":"2025-10-21T23:53:44.31362-07:00","updated_at":"2025-10-22T11:56:36.523529-07:00","closed_at":"2025-10-18T09:41:18.209717-07:00"}
 {"id":"bd-9","title":"Test issue 2","description":"","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-21T23:53:44.31362-07:00","updated_at":"2025-10-22T11:56:36.523753-07:00","closed_at":"2025-10-21T22:06:41.257019-07:00","labels":["test-label"]}