doctor: add git hygiene checks and DB integrity auto-fix

Co-authored-by: factory-droid[bot] <138933559+factory-droid[bot]@users.noreply.github.com>

cmd/bd/doctor.go

@@ -373,6 +373,8 @@ func applyFixList(path string, fixes []doctorCheck) {
 			err = fix.Permissions(path)
 		case "Database":
 			err = fix.DatabaseVersion(path)
+		case "Database Integrity":
+			err = fix.DatabaseIntegrity(path)
 		case "Schema Compatibility":
 			err = fix.SchemaCompatibility(path)
 		case "Repo Fingerprint":
@@ -750,6 +752,16 @@ func runDiagnostics(path string) doctorResult {
 	result.Checks = append(result.Checks, mergeDriverCheck)
 	// Don't fail overall check for merge driver, just warn
 
+	// Check 15a: Git working tree cleanliness (AGENTS.md hygiene)
+	gitWorkingTreeCheck := convertWithCategory(doctor.CheckGitWorkingTree(path), doctor.CategoryGit)
+	result.Checks = append(result.Checks, gitWorkingTreeCheck)
+	// Don't fail overall check for dirty working tree, just warn
+
+	// Check 15b: Git upstream sync (ahead/behind/diverged)
+	gitUpstreamCheck := convertWithCategory(doctor.CheckGitUpstream(path), doctor.CategoryGit)
+	result.Checks = append(result.Checks, gitUpstreamCheck)
+	// Don't fail overall check for upstream drift, just warn
+
 	// Check 16: Metadata.json version tracking (bd-u4sb)
 	metadataCheck := convertWithCategory(doctor.CheckMetadataVersionTracking(path, Version), doctor.CategoryMetadata)
 	result.Checks = append(result.Checks, metadataCheck)

cmd/bd/doctor/database.go

@@ -251,6 +251,7 @@ func CheckDatabaseIntegrity(path string) DoctorCheck {
 			Status:  StatusError,
 			Message: "Failed to open database for integrity check",
 			Detail:  err.Error(),
+			Fix:     "Run 'bd doctor --fix' to back up the corrupt DB and rebuild from JSONL (if available), or restore from backup",
 		}
 	}
 	defer db.Close()
@@ -264,6 +265,7 @@ func CheckDatabaseIntegrity(path string) DoctorCheck {
 			Status:  StatusError,
 			Message: "Failed to run integrity check",
 			Detail:  err.Error(),
+			Fix:     "Run 'bd doctor --fix' to back up the corrupt DB and rebuild from JSONL (if available), or restore from backup",
 		}
 	}
 	defer rows.Close()
@@ -292,7 +294,7 @@ func CheckDatabaseIntegrity(path string) DoctorCheck {
 		Status:  StatusError,
 		Message: "Database corruption detected",
 		Detail:  strings.Join(results, "; "),
-		Fix:     "Database may need recovery. Export with 'bd export' if possible, then restore from backup or reinitialize",
+		Fix:     "Run 'bd doctor --fix' to back up the corrupt DB and rebuild from JSONL (if available), or restore from backup",
 	}
 }
 

cmd/bd/doctor/fix/database_integrity.go

@@ -0,0 +1,134 @@
+package fix
+
+import (
+	"bufio"
+	"encoding/json"
+	"fmt"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"time"
+
+	"github.com/steveyegge/beads/internal/beads"
+	"github.com/steveyegge/beads/internal/configfile"
+	"github.com/steveyegge/beads/internal/utils"
+)
+
+// DatabaseIntegrity attempts to recover from database corruption by:
+//  1. Backing up the corrupt database (and WAL/SHM if present)
+//  2. Re-initializing the database from the git-tracked JSONL export
+//
+// This is intentionally conservative: it will not delete JSONL, and it preserves the
+// original DB as a backup for forensic recovery.
+func DatabaseIntegrity(path string) error {
+	if err := validateBeadsWorkspace(path); err != nil {
+		return err
+	}
+
+	absPath, err := filepath.Abs(path)
+	if err != nil {
+		return fmt.Errorf("failed to resolve path: %w", err)
+	}
+
+	beadsDir := filepath.Join(absPath, ".beads")
+
+	// Resolve database path (respects metadata.json database override).
+	var dbPath string
+	if cfg, err := configfile.Load(beadsDir); err == nil && cfg != nil && cfg.Database != "" {
+		dbPath = cfg.DatabasePath(beadsDir)
+	} else {
+		dbPath = filepath.Join(beadsDir, beads.CanonicalDatabaseName)
+	}
+
+	// Find JSONL source of truth.
+	jsonlPath := ""
+	if cfg, err := configfile.Load(beadsDir); err == nil && cfg != nil {
+		candidate := cfg.JSONLPath(beadsDir)
+		if _, err := os.Stat(candidate); err == nil {
+			jsonlPath = candidate
+		}
+	}
+	if jsonlPath == "" {
+		for _, name := range []string{"issues.jsonl", "beads.jsonl"} {
+			candidate := filepath.Join(beadsDir, name)
+			if _, err := os.Stat(candidate); err == nil {
+				jsonlPath = candidate
+				break
+			}
+		}
+	}
+	if jsonlPath == "" {
+		return fmt.Errorf("cannot auto-recover: no JSONL export found in %s", beadsDir)
+	}
+
+	// Back up corrupt DB and its sidecar files.
+	ts := time.Now().UTC().Format("20060102T150405Z")
+	backupDB := dbPath + "." + ts + ".corrupt.backup.db"
+	if err := os.Rename(dbPath, backupDB); err != nil {
+		return fmt.Errorf("failed to back up database: %w", err)
+	}
+	for _, suffix := range []string{"-wal", "-shm", "-journal"} {
+		sidecar := dbPath + suffix
+		if _, err := os.Stat(sidecar); err == nil {
+			_ = os.Rename(sidecar, backupDB+suffix) // best effort
+		}
+	}
+
+	// Rebuild via bd init, pointing at the same db path.
+	bdBinary, err := getBdBinary()
+	if err != nil {
+		return err
+	}
+
+	args := []string{"--db", dbPath, "init", "--quiet", "--force", "--skip-hooks", "--skip-merge-driver"}
+	if prefix := detectPrefixFromJSONL(jsonlPath); prefix != "" {
+		args = append(args, "--prefix", prefix)
+	}
+
+	cmd := exec.Command(bdBinary, args...) // #nosec G204 -- bdBinary is a validated executable path
+	cmd.Dir = absPath
+	cmd.Stdout = os.Stdout
+	cmd.Stderr = os.Stderr
+	cmd.Env = os.Environ()
+
+	if err := cmd.Run(); err != nil {
+		// Best-effort rollback: if init didn't recreate the db, restore the backup.
+		if _, statErr := os.Stat(dbPath); os.IsNotExist(statErr) {
+			_ = os.Rename(backupDB, dbPath)
+			for _, suffix := range []string{"-wal", "-shm", "-journal"} {
+				_ = os.Rename(backupDB+suffix, dbPath+suffix)
+			}
+		}
+		return fmt.Errorf("failed to rebuild database from JSONL: %w (backup: %s)", err, backupDB)
+	}
+
+	return nil
+}
+
+func detectPrefixFromJSONL(jsonlPath string) string {
+	f, err := os.Open(jsonlPath) // #nosec G304 -- jsonlPath is within the workspace
+	if err != nil {
+		return ""
+	}
+	defer f.Close()
+
+	scanner := bufio.NewScanner(f)
+	for scanner.Scan() {
+		line := scanner.Bytes()
+		if len(line) == 0 {
+			continue
+		}
+		var issue struct {
+			ID string `json:"id"`
+		}
+		if err := json.Unmarshal(line, &issue); err != nil {
+			continue
+		}
+		if issue.ID == "" {
+			continue
+		}
+		return utils.ExtractIssuePrefix(issue.ID)
+	}
+
+	return ""
+}

cmd/bd/doctor/git.go

@@ -78,6 +78,173 @@ func CheckGitHooks() DoctorCheck {
 	}
 }
 
+// CheckGitWorkingTree checks if the git working tree is clean.
+// This helps prevent leaving work stranded (AGENTS.md: keep git state clean).
+func CheckGitWorkingTree(path string) DoctorCheck {
+	cmd := exec.Command("git", "rev-parse", "--git-dir")
+	cmd.Dir = path
+	if err := cmd.Run(); err != nil {
+		return DoctorCheck{
+			Name:    "Git Working Tree",
+			Status:  StatusOK,
+			Message: "N/A (not a git repository)",
+		}
+	}
+
+	cmd = exec.Command("git", "status", "--porcelain")
+	cmd.Dir = path
+	out, err := cmd.Output()
+	if err != nil {
+		return DoctorCheck{
+			Name:    "Git Working Tree",
+			Status:  StatusWarning,
+			Message: "Unable to check git status",
+			Detail:  err.Error(),
+			Fix:     "Run 'git status' and commit/stash changes before syncing",
+		}
+	}
+
+	status := strings.TrimSpace(string(out))
+	if status == "" {
+		return DoctorCheck{
+			Name:    "Git Working Tree",
+			Status:  StatusOK,
+			Message: "Clean",
+		}
+	}
+
+	// Show a small sample of paths for quick debugging.
+	lines := strings.Split(status, "\n")
+	maxLines := 8
+	if len(lines) > maxLines {
+		lines = append(lines[:maxLines], "…")
+	}
+
+	return DoctorCheck{
+		Name:    "Git Working Tree",
+		Status:  StatusWarning,
+		Message: "Uncommitted changes present",
+		Detail:  strings.Join(lines, "\n"),
+		Fix:     "Commit or stash changes, then follow AGENTS.md: git pull --rebase && git push",
+	}
+}
+
+// CheckGitUpstream checks whether the current branch is up to date with its upstream.
+// This catches common "forgot to pull/push" failure modes (AGENTS.md: pull --rebase, push).
+func CheckGitUpstream(path string) DoctorCheck {
+	cmd := exec.Command("git", "rev-parse", "--git-dir")
+	cmd.Dir = path
+	if err := cmd.Run(); err != nil {
+		return DoctorCheck{
+			Name:    "Git Upstream",
+			Status:  StatusOK,
+			Message: "N/A (not a git repository)",
+		}
+	}
+
+	// Detect detached HEAD.
+	cmd = exec.Command("git", "symbolic-ref", "--short", "HEAD")
+	cmd.Dir = path
+	branchOut, err := cmd.Output()
+	if err != nil {
+		return DoctorCheck{
+			Name:    "Git Upstream",
+			Status:  StatusWarning,
+			Message: "Detached HEAD (no branch)",
+			Fix:     "Check out a branch before syncing",
+		}
+	}
+	branch := strings.TrimSpace(string(branchOut))
+
+	cmd = exec.Command("git", "rev-parse", "--abbrev-ref", "--symbolic-full-name", "@{u}")
+	cmd.Dir = path
+	upOut, err := cmd.Output()
+	if err != nil {
+		return DoctorCheck{
+			Name:    "Git Upstream",
+			Status:  StatusWarning,
+			Message: fmt.Sprintf("No upstream configured for %s", branch),
+			Fix:     fmt.Sprintf("Set upstream then push: git push -u origin %s", branch),
+		}
+	}
+	upstream := strings.TrimSpace(string(upOut))
+
+	ahead, aheadErr := gitRevListCount(path, "@{u}..HEAD")
+	behind, behindErr := gitRevListCount(path, "HEAD..@{u}")
+	if aheadErr != nil || behindErr != nil {
+		detailParts := []string{}
+		if aheadErr != nil {
+			detailParts = append(detailParts, "ahead: "+aheadErr.Error())
+		}
+		if behindErr != nil {
+			detailParts = append(detailParts, "behind: "+behindErr.Error())
+		}
+		return DoctorCheck{
+			Name:    "Git Upstream",
+			Status:  StatusWarning,
+			Message: fmt.Sprintf("Unable to compare with upstream (%s)", upstream),
+			Detail:  strings.Join(detailParts, "; "),
+			Fix:     "Run 'git fetch' then check: git status -sb",
+		}
+	}
+
+	if ahead == 0 && behind == 0 {
+		return DoctorCheck{
+			Name:    "Git Upstream",
+			Status:  StatusOK,
+			Message: fmt.Sprintf("Up to date (%s)", upstream),
+			Detail:  fmt.Sprintf("Branch: %s", branch),
+		}
+	}
+
+	if ahead > 0 && behind == 0 {
+		return DoctorCheck{
+			Name:    "Git Upstream",
+			Status:  StatusWarning,
+			Message: fmt.Sprintf("Ahead of upstream by %d commit(s)", ahead),
+			Detail:  fmt.Sprintf("Branch: %s, upstream: %s", branch, upstream),
+			Fix:     "Run 'git push' (AGENTS.md: git pull --rebase && git push)",
+		}
+	}
+
+	if behind > 0 && ahead == 0 {
+		return DoctorCheck{
+			Name:    "Git Upstream",
+			Status:  StatusWarning,
+			Message: fmt.Sprintf("Behind upstream by %d commit(s)", behind),
+			Detail:  fmt.Sprintf("Branch: %s, upstream: %s", branch, upstream),
+			Fix:     "Run 'git pull --rebase' (then re-run bd sync / bd doctor)",
+		}
+	}
+
+	return DoctorCheck{
+		Name:    "Git Upstream",
+		Status:  StatusWarning,
+		Message: fmt.Sprintf("Diverged from upstream (ahead %d, behind %d)", ahead, behind),
+		Detail:  fmt.Sprintf("Branch: %s, upstream: %s", branch, upstream),
+		Fix:     "Run 'git pull --rebase' then 'git push'",
+	}
+}
+
+func gitRevListCount(path string, rangeExpr string) (int, error) {
+	cmd := exec.Command("git", "rev-list", "--count", rangeExpr) // #nosec G204 -- fixed args
+	cmd.Dir = path
+	out, err := cmd.Output()
+	if err != nil {
+		return 0, err
+	}
+	countStr := strings.TrimSpace(string(out))
+	if countStr == "" {
+		return 0, nil
+	}
+
+	var n int
+	if _, err := fmt.Sscanf(countStr, "%d", &n); err != nil {
+		return 0, err
+	}
+	return n, nil
+}
+
 // CheckSyncBranchHookCompatibility checks if pre-push hook is compatible with sync-branch mode.
 // When sync-branch is configured, the pre-push hook must have the sync-branch bypass logic
 // (added in version 0.29.0). Without it, users experience circular "bd sync" failures (issue #532).

cmd/bd/doctor/git_hygiene_test.go

@@ -0,0 +1,172 @@
+package doctor
+
+import (
+	"os"
+	"os/exec"
+	"path/filepath"
+	"strings"
+	"testing"
+)
+
+func mkTmpDirInTmp(t *testing.T, prefix string) string {
+	t.Helper()
+	dir, err := os.MkdirTemp("/tmp", prefix)
+	if err != nil {
+		t.Fatalf("failed to create temp dir: %v", err)
+	}
+	t.Cleanup(func() { _ = os.RemoveAll(dir) })
+	return dir
+}
+
+func runGit(t *testing.T, dir string, args ...string) string {
+	t.Helper()
+	cmd := exec.Command("git", args...)
+	cmd.Dir = dir
+	out, err := cmd.CombinedOutput()
+	if err != nil {
+		t.Fatalf("git %v failed: %v\n%s", args, err, string(out))
+	}
+	return string(out)
+}
+
+func initRepo(t *testing.T, dir string, branch string) {
+	t.Helper()
+	_ = os.MkdirAll(filepath.Join(dir, ".beads"), 0755)
+	runGit(t, dir, "init", "-b", branch)
+	runGit(t, dir, "config", "user.email", "test@test.com")
+	runGit(t, dir, "config", "user.name", "Test User")
+}
+
+func commitFile(t *testing.T, dir, name, content, msg string) {
+	t.Helper()
+	path := filepath.Join(dir, name)
+	if err := os.MkdirAll(filepath.Dir(path), 0755); err != nil {
+		t.Fatalf("mkdir: %v", err)
+	}
+	if err := os.WriteFile(path, []byte(content), 0644); err != nil {
+		t.Fatalf("write file: %v", err)
+	}
+	runGit(t, dir, "add", name)
+	runGit(t, dir, "commit", "-m", msg)
+}
+
+func TestCheckGitWorkingTree(t *testing.T) {
+	t.Run("not a git repo", func(t *testing.T) {
+		dir := mkTmpDirInTmp(t, "bd-git-nt-*")
+		check := CheckGitWorkingTree(dir)
+		if check.Status != StatusOK {
+			t.Fatalf("status=%q want %q", check.Status, StatusOK)
+		}
+		if !strings.Contains(check.Message, "N/A") {
+			t.Fatalf("message=%q want N/A", check.Message)
+		}
+	})
+
+	t.Run("clean", func(t *testing.T) {
+		dir := mkTmpDirInTmp(t, "bd-git-clean-*")
+		initRepo(t, dir, "main")
+		commitFile(t, dir, "README.md", "# test\n", "initial")
+
+		check := CheckGitWorkingTree(dir)
+		if check.Status != StatusOK {
+			t.Fatalf("status=%q want %q (msg=%q)", check.Status, StatusOK, check.Message)
+		}
+	})
+
+	t.Run("dirty", func(t *testing.T) {
+		dir := mkTmpDirInTmp(t, "bd-git-dirty-*")
+		initRepo(t, dir, "main")
+		commitFile(t, dir, "README.md", "# test\n", "initial")
+		if err := os.WriteFile(filepath.Join(dir, "dirty.txt"), []byte("x"), 0644); err != nil {
+			t.Fatalf("write dirty file: %v", err)
+		}
+
+		check := CheckGitWorkingTree(dir)
+		if check.Status != StatusWarning {
+			t.Fatalf("status=%q want %q (msg=%q)", check.Status, StatusWarning, check.Message)
+		}
+	})
+}
+
+func TestCheckGitUpstream(t *testing.T) {
+	t.Run("no upstream", func(t *testing.T) {
+		dir := mkTmpDirInTmp(t, "bd-git-up-*")
+		initRepo(t, dir, "main")
+		commitFile(t, dir, "README.md", "# test\n", "initial")
+
+		check := CheckGitUpstream(dir)
+		if check.Status != StatusWarning {
+			t.Fatalf("status=%q want %q (msg=%q)", check.Status, StatusWarning, check.Message)
+		}
+		if !strings.Contains(check.Message, "No upstream") {
+			t.Fatalf("message=%q want to mention upstream", check.Message)
+		}
+	})
+
+	t.Run("up to date", func(t *testing.T) {
+		dir := mkTmpDirInTmp(t, "bd-git-up2-*")
+		remote := mkTmpDirInTmp(t, "bd-git-remote-*")
+		runGit(t, remote, "init", "--bare")
+
+		initRepo(t, dir, "main")
+		commitFile(t, dir, "README.md", "# test\n", "initial")
+		runGit(t, dir, "remote", "add", "origin", remote)
+		runGit(t, dir, "push", "-u", "origin", "main")
+
+		check := CheckGitUpstream(dir)
+		if check.Status != StatusOK {
+			t.Fatalf("status=%q want %q (msg=%q)", check.Status, StatusOK, check.Message)
+		}
+	})
+
+	t.Run("ahead of upstream", func(t *testing.T) {
+		dir := mkTmpDirInTmp(t, "bd-git-ahead-*")
+		remote := mkTmpDirInTmp(t, "bd-git-remote2-*")
+		runGit(t, remote, "init", "--bare")
+
+		initRepo(t, dir, "main")
+		commitFile(t, dir, "README.md", "# test\n", "initial")
+		runGit(t, dir, "remote", "add", "origin", remote)
+		runGit(t, dir, "push", "-u", "origin", "main")
+
+		commitFile(t, dir, "file2.txt", "x", "local commit")
+
+		check := CheckGitUpstream(dir)
+		if check.Status != StatusWarning {
+			t.Fatalf("status=%q want %q (msg=%q)", check.Status, StatusWarning, check.Message)
+		}
+		if !strings.Contains(check.Message, "Ahead") {
+			t.Fatalf("message=%q want to mention ahead", check.Message)
+		}
+	})
+
+	t.Run("behind upstream", func(t *testing.T) {
+		dir := mkTmpDirInTmp(t, "bd-git-behind-*")
+		remote := mkTmpDirInTmp(t, "bd-git-remote3-*")
+		runGit(t, remote, "init", "--bare")
+
+		initRepo(t, dir, "main")
+		commitFile(t, dir, "README.md", "# test\n", "initial")
+		runGit(t, dir, "remote", "add", "origin", remote)
+		runGit(t, dir, "push", "-u", "origin", "main")
+
+		// Advance remote via another clone.
+		clone := mkTmpDirInTmp(t, "bd-git-clone-*")
+		runGit(t, clone, "clone", remote, ".")
+		runGit(t, clone, "config", "user.email", "test@test.com")
+		runGit(t, clone, "config", "user.name", "Test User")
+		commitFile(t, clone, "remote.txt", "y", "remote commit")
+		runGit(t, clone, "push", "origin", "main")
+
+		// Update tracking refs.
+		runGit(t, dir, "fetch", "origin")
+
+		check := CheckGitUpstream(dir)
+		if check.Status != StatusWarning {
+			t.Fatalf("status=%q want %q (msg=%q)", check.Status, StatusWarning, check.Message)
+		}
+		if !strings.Contains(check.Message, "Behind") {
+			t.Fatalf("message=%q want to mention behind", check.Message)
+		}
+	})
+}

cmd/bd/doctor_repair_test.go

@@ -0,0 +1,147 @@
+package main
+
+import (
+	"encoding/json"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"runtime"
+	"strings"
+	"testing"
+)
+
+func buildBDForTest(t *testing.T) string {
+	t.Helper()
+	exeName := "bd"
+	if runtime.GOOS == "windows" {
+		exeName = "bd.exe"
+	}
+
+	binDir := t.TempDir()
+	exe := filepath.Join(binDir, exeName)
+	cmd := exec.Command("go", "build", "-o", exe, ".")
+	out, err := cmd.CombinedOutput()
+	if err != nil {
+		t.Fatalf("go build failed: %v\n%s", err, string(out))
+	}
+	return exe
+}
+
+func mkTmpDirInTmp(t *testing.T, prefix string) string {
+	t.Helper()
+	dir, err := os.MkdirTemp("/tmp", prefix)
+	if err != nil {
+		t.Fatalf("failed to create temp dir: %v", err)
+	}
+	t.Cleanup(func() { _ = os.RemoveAll(dir) })
+	return dir
+}
+
+func runBDSideDB(t *testing.T, exe, dir, dbPath string, args ...string) (string, error) {
+	t.Helper()
+	fullArgs := []string{"--db", dbPath}
+	if len(args) > 0 && args[0] != "init" {
+		fullArgs = append(fullArgs, "--no-daemon")
+	}
+	fullArgs = append(fullArgs, args...)
+
+	cmd := exec.Command(exe, fullArgs...)
+	cmd.Dir = dir
+	cmd.Env = append(os.Environ(),
+		"BEADS_NO_DAEMON=1",
+		"BEADS_DIR="+filepath.Join(dir, ".beads"),
+	)
+	out, err := cmd.CombinedOutput()
+	return string(out), err
+}
+
+func TestDoctorRepair_CorruptDatabase_RebuildFromJSONL(t *testing.T) {
+	if testing.Short() {
+		t.Skip("skipping slow repair test in short mode")
+	}
+
+	bdExe := buildBDForTest(t)
+	ws := mkTmpDirInTmp(t, "bd-doctor-repair-*")
+	dbPath := filepath.Join(ws, ".beads", "beads.db")
+	jsonlPath := filepath.Join(ws, ".beads", "issues.jsonl")
+
+	if _, err := runBDSideDB(t, bdExe, ws, dbPath, "init", "--prefix", "chaos", "--quiet"); err != nil {
+		t.Fatalf("bd init failed: %v", err)
+	}
+	if _, err := runBDSideDB(t, bdExe, ws, dbPath, "create", "Chaos issue", "-p", "1"); err != nil {
+		t.Fatalf("bd create failed: %v", err)
+	}
+	if _, err := runBDSideDB(t, bdExe, ws, dbPath, "export", "-o", jsonlPath, "--force"); err != nil {
+		t.Fatalf("bd export failed: %v", err)
+	}
+
+	// Corrupt the SQLite file (truncate) and verify doctor reports an integrity error.
+	if err := os.Truncate(dbPath, 128); err != nil {
+		t.Fatalf("truncate db: %v", err)
+	}
+
+	out, err := runBDSideDB(t, bdExe, ws, dbPath, "doctor", "--json")
+	if err == nil {
+		t.Fatalf("expected bd doctor to fail on corrupt db")
+	}
+	jsonStart := strings.Index(out, "{")
+	if jsonStart < 0 {
+		t.Fatalf("doctor output missing JSON: %s", out)
+	}
+	var before doctorResult
+	if err := json.Unmarshal([]byte(out[jsonStart:]), &before); err != nil {
+		t.Fatalf("unmarshal doctor json: %v\n%s", err, out)
+	}
+	var foundIntegrity bool
+	for _, c := range before.Checks {
+		if c.Name == "Database Integrity" {
+			foundIntegrity = true
+			if c.Status != statusError {
+				t.Fatalf("Database Integrity status=%q want %q", c.Status, statusError)
+			}
+		}
+	}
+	if !foundIntegrity {
+		t.Fatalf("Database Integrity check not found")
+	}
+
+	// Attempt auto-repair.
+	out, err = runBDSideDB(t, bdExe, ws, dbPath, "doctor", "--fix", "--yes")
+	if err != nil {
+		t.Fatalf("bd doctor --fix failed: %v\n%s", err, out)
+	}
+
+	// Doctor should now pass.
+	out, err = runBDSideDB(t, bdExe, ws, dbPath, "doctor", "--json")
+	if err != nil {
+		t.Fatalf("bd doctor after fix failed: %v\n%s", err, out)
+	}
+	jsonStart = strings.Index(out, "{")
+	if jsonStart < 0 {
+		t.Fatalf("doctor output missing JSON: %s", out)
+	}
+	var after doctorResult
+	if err := json.Unmarshal([]byte(out[jsonStart:]), &after); err != nil {
+		t.Fatalf("unmarshal doctor json: %v\n%s", err, out)
+	}
+	if !after.OverallOK {
+		t.Fatalf("expected overall_ok=true after repair")
+	}
+
+	// Data should still be present.
+	out, err = runBDSideDB(t, bdExe, ws, dbPath, "list", "--json")
+	if err != nil {
+		t.Fatalf("bd list failed after repair: %v\n%s", err, out)
+	}
+	jsonStart = strings.Index(out, "[")
+	if jsonStart < 0 {
+		t.Fatalf("list output missing JSON array: %s", out)
+	}
+	var issues []map[string]any
+	if err := json.Unmarshal([]byte(out[jsonStart:]), &issues); err != nil {
+		t.Fatalf("unmarshal list json: %v\n%s", err, out)
+	}
+	if len(issues) != 1 {
+		t.Fatalf("expected 1 issue after repair, got %d", len(issues))
+	}
+}

internal/hooks/hooks_test.go

@@ -336,8 +336,8 @@ func TestRun_Async(t *testing.T) {
 	outputFile := filepath.Join(tmpDir, "async_output.txt")
 
 	// Create a hook that writes to a file
-	hookScript := `#!/bin/sh
+	hookScript := "#!/bin/sh\n" +
-echo "async" > ` + outputFile
+		"echo \"async\" > \"" + outputFile + "\"\n"
 	if err := os.WriteFile(hookPath, []byte(hookScript), 0755); err != nil {
 		t.Fatalf("Failed to create hook file: %v", err)
 	}
@@ -348,15 +348,17 @@ echo "async" > ` + outputFile
 	// Run should return immediately
 	runner.Run(EventClose, issue)
 
-	// Wait for the async hook to complete with retries
+	// Wait for the async hook to complete with retries.
+	// Under high test load the goroutine scheduling + exec can be delayed.
 	var output []byte
 	var err error
-	for i := 0; i < 10; i++ {
+	deadline := time.Now().Add(3 * time.Second)
-		time.Sleep(100 * time.Millisecond)
+	for time.Now().Before(deadline) {
 		output, err = os.ReadFile(outputFile)
 		if err == nil {
 			break
 		}
+		time.Sleep(50 * time.Millisecond)
 	}
 
 	if err != nil {

internal/syncbranch/worktree_sync_test.go

@@ -392,7 +392,7 @@ func setupTestRepoWithRemote(t *testing.T) string {
 	}
 
 	// Initialize git repo
-	runGit(t, tmpDir, "init")
+	runGit(t, tmpDir, "init", "-b", "master")
 	runGit(t, tmpDir, "config", "user.email", "test@test.com")
 	runGit(t, tmpDir, "config", "user.name", "Test User")
 
@@ -413,4 +413,3 @@ func setupTestRepoWithRemote(t *testing.T) string {
 
 	return tmpDir
 }
-