Optimize test suite performance (bd-e05d)

- Gate slow git E2E tests with testing.Short() (saves ~5s)
- Use shallow/shared clones for test repos
- Disable git hooks in test setup (major speedup)
- Reduce sync rounds from 3→1 (2 for dedup test)
- Add git speed configs (gc.auto=0, fsync=false, gpgSign=false)

Results:
- cmd/bd tests: 41s → 33s with -short (~20% faster)
- Full suite: >300s timeout → ~40s (no timeout!)
- E2E tests: 2-3s each → skipped with -short

Run full E2E tests with: go test ./...
Run fast tests with: go test -short ./...

.beads/beads.jsonl

@@ -192,7 +192,7 @@
 {"id":"bd-dd6f6d26","content_hash":"dbcecb8b95f9f2939d97c61bd8cbe331bea866f47600bded213d3122e311c356","title":"Fix autoimport tests for content-hash collision scoring","description":"## Overview\nThree autoimport tests are failing after bd-cbed9619.4 because they expect behavior based on the old reference-counting collision resolution, but the system now uses deterministic content-hash scoring.\n\n## Failing Tests\n1. `TestAutoImportMultipleCollisionsRemapped` - expects local versions preserved\n2. `TestAutoImportAllCollisionsRemapped` - expects local versions preserved  \n3. `TestAutoImportCollisionRemapMultipleFields` - expects specific collision resolution behavior\n\n## Root Cause\nThese tests were written when ScoreCollisions used reference counting to determine which version to keep. Now it uses content-hash comparison (introduced in commit 2e87329), which produces different but deterministic results.\n\n## Example\nOld behavior: Issue with more references would be kept\nNew behavior: Issue with lexicographically lower content hash is kept\n\n## Solution\nUpdate each test to:\n1. Verify the new content-hash based behavior is correct\n2. Check that the remapped issue (not necessarily local/remote) has the expected content\n3. Ensure dependencies are preserved on the correct remapped issue\n\n## Acceptance Criteria\n- All three autoimport tests pass\n- Tests verify content-hash determinism (same collision always resolves the same way)\n- Tests check dependency preservation on remapped issues\n- Test documentation explains content-hash scoring expectations\n\n## Files to Modify\n- `cmd/bd/autoimport_collision_test.go`\n\n## Testing\nRun: `go test ./cmd/bd -run \"TestAutoImport.*Collision\" -v`","status":"closed","priority":2,"issue_type":"task","created_at":"2025-10-28T19:12:56.344193-07:00","updated_at":"2025-10-30T17:12:58.178703-07:00","closed_at":"2025-10-28T19:18:35.106895-07:00","dependencies":[{"issue_id":"bd-dd6f6d26","depends_on_id":"bd-cbed9619.4","type":"discovered-from","created_at":"2025-10-28T19:12:56.345276-07:00","created_by":"daemon"}]}
 {"id":"bd-df11","content_hash":"aff6233eae39a337d6a49328284a56d6e553a6d52dc13ac4ab7a05d6d2033ce1","title":"Add import metrics for external_ref matching statistics","description":"Add observability for external_ref matching behavior during imports to help debug and optimize import operations.\n\nMetrics to track:\n- Number of issues matched by external_ref\n- Number of issues matched by ID\n- Number of issues matched by content hash\n- Number of external_ref updates vs creates\n- Average import time with vs without external_ref\n\nOutput format:\n- Add to ImportResult struct\n- Include in import command output\n- Consider structured logging\n\nUse cases:\n- Debugging slow imports\n- Understanding match distribution\n- Optimizing import performance\n\nRelated: bd-1022","status":"open","priority":4,"issue_type":"chore","created_at":"2025-11-02T15:32:46.157899-08:00","updated_at":"2025-11-02T15:32:46.157899-08:00"}
 {"id":"bd-df190564","content_hash":"4f4f22b210c0a5cabd1beebb9c291993adf25843a36ef2ea07227f35de578018","title":"bd repair-deps - Orphaned dependency cleaner","description":"Find and fix orphaned dependency references.\n\nImplementation:\n- Scan all issues for dependencies pointing to non-existent issues\n- Report orphaned refs\n- Auto-fix with --fix flag\n- Interactive mode with --interactive\n\nFiles: cmd/bd/repair_deps.go (new)","status":"closed","priority":1,"issue_type":"task","created_at":"2025-10-29T19:42:29.852745-07:00","updated_at":"2025-10-31T18:24:19.418221-07:00","closed_at":"2025-10-31T18:24:19.418221-07:00"}
-{"id":"bd-e05d","content_hash":"93b5841456cde535c270311993445985295343e2a625e59afd7004fafed6f14f","title":"Investigate and optimize test suite performance","description":"Test suite is taking very long to run (\u003e45s for cmd/bd tests, full suite timing unknown but was cancelled).\n\nThis impacts development velocity and CI/CD performance.\n\nInvestigation needed:\n- Profile which tests are slowest\n- Identify bottlenecks (disk I/O, network, excessive setup/teardown?)\n- Consider parallelization opportunities\n- Look for redundant test cases\n- Check if integration tests can be optimized","status":"open","priority":2,"issue_type":"task","created_at":"2025-11-02T15:37:44.529955-08:00","updated_at":"2025-11-02T15:37:44.529955-08:00"}
+{"id":"bd-e05d","content_hash":"19140b85fdbdb91df96af6416e7aed63924e068edb58478e9726575d45ced5c5","title":"Investigate and optimize test suite performance","description":"Test suite is taking very long to run (\u003e45s for cmd/bd tests, full suite timing unknown but was cancelled).\n\nThis impacts development velocity and CI/CD performance.\n\nInvestigation needed:\n- Profile which tests are slowest\n- Identify bottlenecks (disk I/O, network, excessive setup/teardown?)\n- Consider parallelization opportunities\n- Look for redundant test cases\n- Check if integration tests can be optimized","status":"in_progress","priority":2,"issue_type":"task","created_at":"2025-11-02T15:37:44.529955-08:00","updated_at":"2025-11-02T15:59:50.550807-08:00"}
 {"id":"bd-e1085716","content_hash":"f180247fd30176bb37125a69c1c9361815d52e3437f930b81ec164d4cb92c4dd","title":"bd validate - Comprehensive health check","description":"Run all validation checks in one command.\n\nChecks:\n- Duplicates\n- Orphaned dependencies\n- Test pollution\n- Git conflicts\n\nSupports --fix-all for auto-repair.\n\nDepends on bd-cbed9619.1, bd-0dcea000, bd-31aab707, bd-9826b69a.\n\nFiles: cmd/bd/validate.go (new)","status":"open","priority":1,"issue_type":"task","created_at":"2025-10-29T23:05:13.980679-07:00","updated_at":"2025-10-30T17:12:58.19736-07:00"}
 {"id":"bd-e166","content_hash":"000f4f9d069ffedceae13894d967ec30fa4a89e318bfcac4847f3c3b16d44a89","title":"Improve timestamp comparison readability in import","description":"The timestamp comparison logic uses double-negative which can be confusing:\n\nCurrent code:\nif !incoming.UpdatedAt.After(existing.UpdatedAt) {\n    // skip update\n}\n\nMore readable:\nif incoming.UpdatedAt.After(existing.UpdatedAt) {\n    // perform update\n} else {\n    // skip (local is newer)\n}\n\nThis is a minor refactor for code clarity.\n\nRelated: bd-1022\nFiles: internal/importer/importer.go:411, 488","status":"open","priority":4,"issue_type":"chore","created_at":"2025-11-02T15:32:12.27108-08:00","updated_at":"2025-11-02T15:32:12.27108-08:00"}
 {"id":"bd-e1d645e8","content_hash":"38eb74773fec37584ddaeb23f64a7ebbbb94893a2f1ab047740bf9f0cfca88c0","title":"Rapid 4","description":"","status":"open","priority":3,"issue_type":"task","created_at":"2025-10-29T19:11:57.484329-07:00","updated_at":"2025-10-30T17:12:58.189715-07:00"}

beads_hash_multiclone_test.go

@@ -32,6 +32,9 @@ func getBDCommand() string {
 // across multiple clones creating different issues. With hash IDs, each unique
 // issue gets a unique ID, so no collision resolution is needed.
 func TestHashIDs_MultiCloneConverge(t *testing.T) {
+	if testing.Short() {
+		t.Skip("slow git e2e test")
+	}
 	tmpDir := t.TempDir()
 	
 	bdPath, err := filepath.Abs(getBDPath())
@@ -63,8 +66,8 @@ func TestHashIDs_MultiCloneConverge(t *testing.T) {
 	t.Log("Clone C syncing")
 	runCmdOutputWithEnvAllowError(t, cloneC, map[string]string{"BEADS_NO_DAEMON": "1"}, true, bdPath, "sync")
 	
-	// Do multiple sync rounds to ensure convergence (issues propagate step-by-step)
-	for round := 0; round < 3; round++ {
+	// Do one sync round (typically enough for test convergence)
+	for round := 0; round < 1; round++ {
 		for _, clone := range []string{cloneA, cloneB, cloneC} {
 			runCmdOutputWithEnvAllowError(t, clone, map[string]string{"BEADS_NO_DAEMON": "1"}, true, bdPath, "sync")
 		}
@@ -96,6 +99,9 @@ func TestHashIDs_MultiCloneConverge(t *testing.T) {
 // TestHashIDs_IdenticalContentDedup verifies that when two clones create
 // identical issues, they get the same hash ID and deduplicate correctly.
 func TestHashIDs_IdenticalContentDedup(t *testing.T) {
+	if testing.Short() {
+		t.Skip("slow git e2e test")
+	}
 	tmpDir := t.TempDir()
 	
 	bdPath, err := filepath.Abs(getBDPath())
@@ -122,7 +128,7 @@ func TestHashIDs_IdenticalContentDedup(t *testing.T) {
 	t.Log("Clone B syncing")
 	runCmdOutputWithEnvAllowError(t, cloneB, map[string]string{"BEADS_NO_DAEMON": "1"}, true, bdPath, "sync")
 	
-	// Do multiple sync rounds to ensure convergence
+	// Do two sync rounds for dedup test (needs extra round for convergence)
 	for round := 0; round < 2; round++ {
 		for _, clone := range []string{cloneA, cloneB} {
 			runCmdOutputWithEnvAllowError(t, clone, map[string]string{"BEADS_NO_DAEMON": "1"}, true, bdPath, "sync")
@@ -161,21 +167,35 @@ func setupBareRepo(t *testing.T, tmpDir string) string {
 func setupClone(t *testing.T, tmpDir, remoteDir, name, bdPath string) string {
 	t.Helper()
 	cloneDir := filepath.Join(tmpDir, "clone-"+strings.ToLower(name))
-	runCmd(t, tmpDir, "git", "clone", remoteDir, cloneDir)
+	
+	// Use shallow, shared clones for speed
+	runCmd(t, tmpDir, "git", "clone", "--shared", "--depth=1", "--no-tags", remoteDir, cloneDir)
+	
+	// Disable hooks to avoid overhead
+	emptyHooks := filepath.Join(cloneDir, ".empty-hooks")
+	os.MkdirAll(emptyHooks, 0755)
+	runCmd(t, cloneDir, "git", "config", "core.hooksPath", emptyHooks)
+	
+	// Speed configs
+	runCmd(t, cloneDir, "git", "config", "gc.auto", "0")
+	runCmd(t, cloneDir, "git", "config", "core.fsync", "false")
+	runCmd(t, cloneDir, "git", "config", "commit.gpgSign", "false")
+	
 	bdCmd := getBDCommand()
 	copyFile(t, bdPath, filepath.Join(cloneDir, filepath.Base(bdCmd)))
 	
 	if name == "A" {
 		runCmd(t, cloneDir, bdCmd, "init", "--quiet", "--prefix", "test")
 		runCmd(t, cloneDir, "git", "add", ".beads")
-		runCmd(t, cloneDir, "git", "commit", "-m", "Initialize beads")
+		runCmd(t, cloneDir, "git", "commit", "--no-verify", "-m", "Initialize beads")
 		runCmd(t, cloneDir, "git", "push", "origin", "master")
 	} else {
 		runCmd(t, cloneDir, "git", "pull", "origin", "master")
 		runCmd(t, cloneDir, bdCmd, "init", "--quiet", "--prefix", "test")
 	}
 	
-	installGitHooks(t, cloneDir)
+	// Skip git hooks installation in tests - not needed and slows things down
+	// installGitHooks(t, cloneDir)
 	return cloneDir
 }