Fix CI test failures (bd-1231)

- Always recompute content_hash in importer to avoid stale hashes from JSONL
- Add .gitignore to test repos to prevent database files from being tracked
- Fix daemon auto-import test to use correct RPC operation ('show' not 'get_issue')
- Set last_import_time metadata in test helper to enable staleness check
- Add filesystem settle delay after git pull in tests

Root cause: CloseIssue updates status but not content_hash, so importer
thought issues were unchanged. Always recomputing content_hash fixes this.

Amp-Thread-ID: https://ampcode.com/threads/T-63ef3a7d-8efe-472d-97ed-6ac95bd8318b
Co-authored-by: Amp <amp@ampcode.com>

.beads/beads.jsonl

@@ -12,6 +12,7 @@
 {"id":"bd-0dcea000","content_hash":"a6fc218b07d270e3498957525c39a869f7c850d687339b6d758a246be20c9591","title":"Add tests for internal/importer package","description":"Currently 0.0% coverage. Need tests for JSONL import logic including collision detection and resolution.","status":"open","priority":2,"issue_type":"task","created_at":"2025-10-29T14:06:21.071024-07:00","updated_at":"2025-10-30T17:12:58.183211-07:00","dependencies":[{"issue_id":"bd-0dcea000","depends_on_id":"bd-cbed9619.5","type":"blocks","created_at":"2025-10-29T19:52:05.531279-07:00","created_by":"import-remap"},{"issue_id":"bd-0dcea000","depends_on_id":"bd-cbed9619.4","type":"blocks","created_at":"2025-10-29T19:52:05.53166-07:00","created_by":"import-remap"}]}
 {"id":"bd-0e1f2b1b","content_hash":"c0b1677fe3f4aa3f395ae4d79bff5362632d5db26477bf571c09f9177b8741ef","title":"Event-driven daemon architecture","description":"Replace 5-second polling sync loop with event-driven architecture that reacts instantly to changes. Eliminates stale data issues while reducing CPU ~60%. Key components: FileWatcher (fsnotify), Debouncer (500ms), RPC mutation events, optional git hooks. Target latency: \u003c500ms (vs 5000ms). See event_driven_daemon.md for full design.","status":"closed","priority":1,"issue_type":"epic","created_at":"2025-10-28T16:20:02.430479-07:00","updated_at":"2025-10-30T17:12:58.221424-07:00","closed_at":"2025-10-28T16:30:26.631191-07:00"}
 {"id":"bd-11e0","content_hash":"591db3f5674cf7f79b1f50d6b8d83fe60e495f02a21e181c9c63d8da88308d58","title":"Database import silently fails when daemon version != CLI version","description":"","status":"closed","priority":1,"issue_type":"bug","created_at":"2025-10-31T21:08:09.096749-07:00","updated_at":"2025-11-01T19:29:35.267817-07:00","closed_at":"2025-11-01T19:29:35.267817-07:00"}
+{"id":"bd-1231","content_hash":"505d3a61a2c22cc4292a717c04906b9cfcac6ee20e4b7af09c9ac6077b5e0921","title":"CI failing on all 3/4 test jobs despite individual tests passing","description":"CI has been broken for a day+ with mysterious test failures. Issue #173 on GitHub tracks this.\n\n## Current Status\n- **Lint job**: ✅ PASSING\n- **Test (Linux)**: ❌ FAILING (exit code 1)\n- **Test (Windows)**: ❌ FAILING (exit code 1)\n- **Test Nix Flake**: ❌ FAILING (exit code 1)\n\n## Key Observations\nAll three failing jobs show identical pattern:\n- Individual test output shows PASS for every test\n- Final result: `FAIL github.com/steveyegge/beads/cmd/bd`\n- Exit code 1 despite no visible test failures\n- Last visible test output before failure: \"No Reason Issue\" test (TestCloseCommand/close_without_reason)\n\n## Investigation So Far\n1. All tests appear to pass when examined individually\n2. Likely causes:\n   - Race detector finding data races during test cleanup (`-race` flag)\n   - Panic/error occurring after main tests complete\n   - Test harness issue not reporting actual failure\n   - Possible regression from PR #203 (dependency_type changes)\n\n## Recent CI Runs\n- Run 19015040655 (latest): 3/4 failing\n- Multiple recent commits tried to fix Windows/lint issues\n- Agent on rrnewton/beads fork attempting fixes (2/4 passing there)\n\n## Next Steps\n1. Run tests locally with `-race -v` to see full output\n2. Check for unreported test failures or panics\n3. Examine test cleanup/teardown code\n4. Review recent changes around close command tests\n5. Consider if race detector is too sensitive or catching real issues","status":"in_progress","priority":0,"issue_type":"bug","created_at":"2025-11-02T08:42:16.142128-08:00","updated_at":"2025-11-02T08:42:54.327496-08:00","external_ref":"https://github.com/steveyegge/beads/issues/173"}
 {"id":"bd-12c2","content_hash":"caa7a5f6e61a9b1c872f5462e53ed0ecdedc8835265ba6b7c7ef2100fa6448ae","title":"Add comprehensive tests for show.go commands (show, update, edit, close)","description":"Need to add tests for cmd/bd/show.go which contains show, update, edit, and close commands.\n\n**Challenge**: The existing test patterns use rootCmd.SetArgs() and rootCmd.Execute(), but the global `store` variable needs to match what the commands use. Initial attempt created tests that failed with \"no issue found\" because the test's store instance wasn't the same as the command's store.\n\n**Files to test**:\n- show.go (contains showCmd, updateCmd, editCmd, closeCmd)\n\n**Coverage needed**:\n- show command (single issue, multiple issues, JSON output, with dependencies, with labels, with compaction)\n- update command (status, priority, title, assignee, description, multiple fields, multiple issues)\n- edit command (requires $EDITOR, may need mocking)\n- close command (single issue, multiple issues, with reason, JSON output)\n\n**Test approach**:\n1. Study working test patterns in init_test.go, list_test.go, etc.\n2. Ensure BEADS_NO_DAEMON=1 is set\n3. Properly initialize database with bd init\n4. Use the command's global store, not a separate instance\n5. May need to reset global state between tests\n\n**Success criteria**: \n- All test functions pass\n- Coverage for show.go increases significantly\n- Tests follow existing patterns in cmd/bd/*_test.go","status":"closed","priority":0,"issue_type":"task","created_at":"2025-10-31T20:08:40.545173-07:00","updated_at":"2025-10-31T20:19:22.411066-07:00","closed_at":"2025-10-31T20:19:22.411066-07:00"}
 {"id":"bd-1445","content_hash":"20fa939366a39e352f5c2ddad5705ab13559440366eebcb4f32db42a5660dfdc","title":"Create shared insert/event/dirty helpers","description":"Create issues.go (insertIssue/insertIssues), events.go (recordCreatedEvent/recordCreatedEvents), dirty.go (markDirty/markDirtyBatch). Refactor single and bulk create paths to use these.","status":"open","priority":1,"issue_type":"task","created_at":"2025-11-01T11:41:14.882142-07:00","updated_at":"2025-11-01T11:41:14.882142-07:00"}
 {"id":"bd-17fa2d21","content_hash":"139511c299c2fa977d11d5496245b23f4c27fe785fd4fc94470a35b0e4a01a0a","title":"Batch test 2","description":"","status":"closed","priority":2,"issue_type":"task","created_at":"2025-10-29T15:29:01.877052-07:00","updated_at":"2025-10-31T12:00:43.183657-07:00","closed_at":"2025-10-31T12:00:43.183657-07:00"}
@@ -62,7 +63,7 @@
 {"id":"bd-4d80b7b1","content_hash":"0cad3e22d722ff045a29f218962fb00bd8265a1cfc82c5b70f29ffe1a40e4088","title":"Investigate and upgrade to modernc.org/sqlite 1.39.1+","description":"We had to pin modernc.org/sqlite to v1.38.2 due to a FOREIGN KEY constraint regression in v1.39.1 (SQLite 3.50.4).\n\n**Issue:** [deleted:bd-cb64c226.2], GH #144\n\n**Symptom:** CloseIssue fails with \"FOREIGN KEY constraint failed (787)\" when called via MCP/daemon, but works fine via CLI.\n\n**Root Cause:** Unknown - likely stricter FK enforcement in SQLite 3.50.4 or modernc.org wrapper changes.\n\n**Workaround:** Pinned to v1.38.2 (SQLite 3.49.x)\n\n**TODO:**\n1. Monitor modernc.org/sqlite releases for fixes\n2. Check SQLite 3.50.5+ changelogs for FK-related fixes\n3. Investigate why daemon mode fails but CLI succeeds (connection reuse? transaction isolation?)\n4. Consider filing upstream issue with reproducible test case\n5. Upgrade when safe","status":"open","priority":2,"issue_type":"task","created_at":"2025-10-24T11:49:12.836292-07:00","updated_at":"2025-10-30T17:12:58.211344-07:00"}
 {"id":"bd-4e21b5ad","content_hash":"8029d0c5b14261648d3d17d8bc26413183962eab2875772cd2585db92c0104a6","title":"Add test case for symmetric collision (both clones create same ID simultaneously)","description":"TestTwoCloneCollision demonstrates the problem, but we need a simpler unit test for the collision resolver itself.\n\nTest should verify:\n- Two issues with same ID, different content\n- Content hash determines winner deterministically  \n- Result is same regardless of which clone imports first\n- No title swapping occurs\n\nThis can be a simpler test than the full integration test.","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-29T17:46:10.046999-07:00","updated_at":"2025-10-31T12:00:43.196705-07:00","closed_at":"2025-10-31T12:00:43.196705-07:00"}
 {"id":"bd-4f582ec8","content_hash":"02e00868aecbd17486f988a5927a68a07bc309978b33568361559a182eadb2cc","title":"Test auto-start in fred","description":"","status":"closed","priority":3,"issue_type":"task","created_at":"2025-10-30T17:46:16.668088-07:00","updated_at":"2025-10-31T12:00:43.185723-07:00","closed_at":"2025-10-31T12:00:43.185723-07:00"}
-{"id":"bd-4ff2","content_hash":"f7477feb5757bb9663e792f4b740028a786a4ec5f0ec38c131aa4dda0dc7697b","title":"Fix CI failures before 0.21.3 release","description":"CI is failing on multiple jobs:\n1. Nix flake: Tests fail due to missing git in build environment\n2. Windows tests: Need to check what's failing\n3. Linux tests: Need to check what's failing\n4. Linter errors: Many unchecked errors need fixing\n\nNeed to fix before tagging v0.21.3 release.","status":"open","priority":0,"issue_type":"bug","created_at":"2025-11-01T23:52:09.244763-07:00","updated_at":"2025-11-01T23:52:09.244763-07:00"}
+{"id":"bd-4ff2","content_hash":"c245bd7fec00b7a899ace53a6f7f518252c93692fd2b74e5adf2a8b1c90f87b5","title":"Fix CI failures before 0.21.3 release","description":"CI is failing on multiple jobs:\n1. Nix flake: Tests fail due to missing git in build environment\n2. Windows tests: Need to check what's failing\n3. Linux tests: Need to check what's failing\n4. Linter errors: Many unchecked errors need fixing\n\nNeed to fix before tagging v0.21.3 release.","notes":"Fixed linter errors (errcheck, misspell), Nix flake git dependency, and import database discovery bug. Tests still failing - need to investigate further.","status":"in_progress","priority":0,"issue_type":"bug","created_at":"2025-11-01T23:52:09.244763-07:00","updated_at":"2025-11-02T00:21:14.149364-07:00"}
 {"id":"bd-5314bddf","content_hash":"bbaf3bd26766fb78465900c455661a3608ab1d1485cb964d12229badf138753a","title":"bd detect-pollution - Test pollution detector","description":"Detect test issues that leaked into production DB.\n\nPattern matching for:\n- Titles starting with 'test', 'benchmark', 'sample'\n- Sequential numbering (test-1, test-2)\n- Generic descriptions\n- Created in rapid succession\n\nOptional AI scoring for confidence.\n\nFiles: cmd/bd/detect_pollution.go (new)","status":"open","priority":1,"issue_type":"task","created_at":"2025-10-28T14:48:17.466906-07:00","updated_at":"2025-10-30T17:12:58.219307-07:00"}
 {"id":"bd-5599","content_hash":"c48839a6f7f5ca4083ced2f0f47cd250046146032555a14864ac3469a42bb76b","title":"Fix TestListCommand duplicate dependency constraint violation","description":"","status":"closed","priority":2,"issue_type":"bug","created_at":"2025-10-31T21:27:05.557548-07:00","updated_at":"2025-10-31T21:27:11.429018-07:00","closed_at":"2025-10-31T21:27:11.429018-07:00"}
 {"id":"bd-581b80b3","content_hash":"04c4d952852ae2673e551d9776698c52b0189754ac5f9ca295bed464a5b86a43","title":"bd find-duplicates - AI-powered duplicate detection","description":"Find semantically duplicate issues.\n\nApproaches:\n1. Mechanical: Exact title/description matching\n2. Embeddings: Cosine similarity (cheap, scalable)\n3. AI: LLM-based semantic comparison (expensive, accurate)\n\nUses embeddings by default for \u003e100 issues.\n\nFiles: cmd/bd/find_duplicates.go (new)","status":"open","priority":1,"issue_type":"task","created_at":"2025-10-29T20:49:49.126801-07:00","updated_at":"2025-10-30T17:12:58.218673-07:00"}

cmd/bd/daemon_autoimport_test.go

@@ -131,6 +131,9 @@ func TestDaemonAutoImportAfterGitPull(t *testing.T) {
 		// Agent B does git pull (updates JSONL on disk)
 		runGitCmd(t, clone2Dir, "pull")
 		
+		// Wait for filesystem to settle after git operations
+		time.Sleep(50 * time.Millisecond)
+		
 		// Start daemon server in clone2
 		socketPath := filepath.Join(clone2BeadsDir, "bd.sock")
 		os.Remove(socketPath) // Ensure clean state
@@ -329,6 +332,9 @@ func TestDaemonAutoImportDataCorruption(t *testing.T) {
 	// 2. Agent B does git pull (JSONL updated on disk)
 	runGitCmd(t, clone2Dir, "pull")
 	
+	// Wait for filesystem to settle after git operations
+	time.Sleep(50 * time.Millisecond)
+	
 	// 3. Agent B daemon exports STALE data (if auto-import doesn't work)
 	// This would overwrite Agent A's closure with old "open" status
 	
@@ -364,7 +370,7 @@ func TestDaemonAutoImportDataCorruption(t *testing.T) {
 	
 	client.SetDatabasePath(clone2DBPath)
 	
-	resp, err := client.Execute("get_issue", map[string]string{"id": issueID})
+	resp, err := client.Execute("show", map[string]string{"id": issueID})
 	if err != nil {
 		t.Fatalf("Failed to get issue: %v", err)
 	}

cmd/bd/git_sync_test.go

@@ -211,6 +211,18 @@ func configureGit(t *testing.T, dir string) {
 	runGitCmd(t, dir, "config", "user.email", "test@example.com")
 	runGitCmd(t, dir, "config", "user.name", "Test User")
 	runGitCmd(t, dir, "config", "pull.rebase", "false")
+	
+	// Create .gitignore to prevent test database files from being tracked
+	gitignorePath := filepath.Join(dir, ".gitignore")
+	gitignoreContent := `# Test database files
+*.db
+*.db-journal
+*.db-wal
+*.db-shm
+`
+	if err := os.WriteFile(gitignorePath, []byte(gitignoreContent), 0644); err != nil {
+		t.Fatalf("Failed to create .gitignore: %v", err)
+	}
 }
 
 func exportIssuesToJSONL(ctx context.Context, store *sqlite.SQLiteStorage, jsonlPath string) error {
@@ -284,6 +296,11 @@ func importJSONLToStore(ctx context.Context, store *sqlite.SQLiteStorage, dbPath
 		}
 	}
 	
+	// Set last_import_time metadata so staleness check works
+	if err := store.SetMetadata(ctx, "last_import_time", time.Now().Format(time.RFC3339)); err != nil {
+		return err
+	}
+	
 	return nil
 }
 

internal/importer/importer.go

@@ -61,10 +61,9 @@ func ImportIssues(ctx context.Context, dbPath string, store storage.Storage, iss
 	}
 
 	// Compute content hashes for all incoming issues (bd-95)
+	// Always recompute to avoid stale/incorrect JSONL hashes (bd-1231)
 	for _, issue := range issues {
-		if issue.ContentHash == "" {
+		issue.ContentHash = issue.ComputeContentHash()
-			issue.ContentHash = issue.ComputeContentHash()
-		}
 	}
 
 	// Get or create SQLite store