tests: add chaos doctor repair coverage and stabilize git init

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

cmd/bd/daemon_autoimport_test.go

@@ -38,7 +38,7 @@ func TestDaemonAutoImportAfterGitPull(t *testing.T) {
 	}
 
 	// Initialize remote git repo
-	runGitCmd(t, remoteDir, "init", "--bare")
+	runGitCmd(t, remoteDir, "init", "--bare", "-b", "master")
 
 	// Create "clone1" repository (Agent A)
 	clone1Dir := filepath.Join(tempDir, "clone1")
@@ -277,7 +277,7 @@ func TestDaemonAutoImportDataCorruption(t *testing.T) {
 	// Setup remote and two clones
 	remoteDir := filepath.Join(tempDir, "remote")
 	os.MkdirAll(remoteDir, 0750)
-	runGitCmd(t, remoteDir, "init", "--bare")
+	runGitCmd(t, remoteDir, "init", "--bare", "-b", "master")
 
 	clone1Dir := filepath.Join(tempDir, "clone1")
 	runGitCmd(t, tempDir, "clone", remoteDir, clone1Dir)

cmd/bd/daemon_sync_branch_test.go

@@ -48,12 +48,12 @@ func TestSyncBranchCommitAndPush_NotConfigured(t *testing.T) {
 
 	// Create test issue
 	issue := &types.Issue{
-		Title:       "Test issue",
+		Title:     "Test issue",
-		Status:      types.StatusOpen,
+		Status:    types.StatusOpen,
-		Priority:    1,
+		Priority:  1,
-		IssueType:   types.TypeTask,
+		IssueType: types.TypeTask,
-		CreatedAt:   time.Now(),
+		CreatedAt: time.Now(),
-		UpdatedAt:   time.Now(),
+		UpdatedAt: time.Now(),
 	}
 	if err := store.CreateIssue(ctx, issue, "test"); err != nil {
 		t.Fatalf("Failed to create issue: %v", err)
@@ -122,12 +122,12 @@ func TestSyncBranchCommitAndPush_Success(t *testing.T) {
 
 	// Create test issue
 	issue := &types.Issue{
-		Title:       "Test sync branch issue",
+		Title:     "Test sync branch issue",
-		Status:      types.StatusOpen,
+		Status:    types.StatusOpen,
-		Priority:    1,
+		Priority:  1,
-		IssueType:   types.TypeTask,
+		IssueType: types.TypeTask,
-		CreatedAt:   time.Now(),
+		CreatedAt: time.Now(),
-		UpdatedAt:   time.Now(),
+		UpdatedAt: time.Now(),
 	}
 	if err := store.CreateIssue(ctx, issue, "test"); err != nil {
 		t.Fatalf("Failed to create issue: %v", err)
@@ -228,12 +228,12 @@ func TestSyncBranchCommitAndPush_EnvOverridesDB(t *testing.T) {
 
 	// Create test issue and export JSONL
 	issue := &types.Issue{
-		Title:       "Env override issue",
+		Title:     "Env override issue",
-		Status:      types.StatusOpen,
+		Status:    types.StatusOpen,
-		Priority:    1,
+		Priority:  1,
-		IssueType:   types.TypeTask,
+		IssueType: types.TypeTask,
-		CreatedAt:   time.Now(),
+		CreatedAt: time.Now(),
-		UpdatedAt:   time.Now(),
+		UpdatedAt: time.Now(),
 	}
 	if err := store.CreateIssue(ctx, issue, "test"); err != nil {
 		t.Fatalf("Failed to create issue: %v", err)
@@ -303,12 +303,12 @@ func TestSyncBranchCommitAndPush_NoChanges(t *testing.T) {
 	}
 
 	issue := &types.Issue{
-		Title:       "Test issue",
+		Title:     "Test issue",
-		Status:      types.StatusOpen,
+		Status:    types.StatusOpen,
-		Priority:    1,
+		Priority:  1,
-		IssueType:   types.TypeTask,
+		IssueType: types.TypeTask,
-		CreatedAt:   time.Now(),
+		CreatedAt: time.Now(),
-		UpdatedAt:   time.Now(),
+		UpdatedAt: time.Now(),
 	}
 	if err := store.CreateIssue(ctx, issue, "test"); err != nil {
 		t.Fatalf("Failed to create issue: %v", err)
@@ -380,12 +380,12 @@ func TestSyncBranchCommitAndPush_WorktreeHealthCheck(t *testing.T) {
 	}
 
 	issue := &types.Issue{
-		Title:       "Test issue",
+		Title:     "Test issue",
-		Status:      types.StatusOpen,
+		Status:    types.StatusOpen,
-		Priority:    1,
+		Priority:  1,
-		IssueType:   types.TypeTask,
+		IssueType: types.TypeTask,
-		CreatedAt:   time.Now(),
+		CreatedAt: time.Now(),
-		UpdatedAt:   time.Now(),
+		UpdatedAt: time.Now(),
 	}
 	if err := store.CreateIssue(ctx, issue, "test"); err != nil {
 		t.Fatalf("Failed to create issue: %v", err)
@@ -497,7 +497,7 @@ func TestSyncBranchPull_Success(t *testing.T) {
 	if err := os.MkdirAll(remoteDir, 0755); err != nil {
 		t.Fatalf("Failed to create remote dir: %v", err)
 	}
-	runGitCmd(t, remoteDir, "init", "--bare")
+	runGitCmd(t, remoteDir, "init", "--bare", "-b", "master")
 
 	// Create clone1 (will push changes)
 	clone1Dir := filepath.Join(tmpDir, "clone1")
@@ -528,12 +528,12 @@ func TestSyncBranchPull_Success(t *testing.T) {
 
 	// Create issue in clone1
 	issue := &types.Issue{
-		Title:       "Test sync pull issue",
+		Title:     "Test sync pull issue",
-		Status:      types.StatusOpen,
+		Status:    types.StatusOpen,
-		Priority:    1,
+		Priority:  1,
-		IssueType:   types.TypeTask,
+		IssueType: types.TypeTask,
-		CreatedAt:   time.Now(),
+		CreatedAt: time.Now(),
-		UpdatedAt:   time.Now(),
+		UpdatedAt: time.Now(),
 	}
 	if err := store1.CreateIssue(ctx, issue, "test"); err != nil {
 		t.Fatalf("Failed to create issue: %v", err)
@@ -639,7 +639,7 @@ func TestSyncBranchIntegration_EndToEnd(t *testing.T) {
 	tmpDir := t.TempDir()
 	remoteDir := filepath.Join(tmpDir, "remote")
 	os.MkdirAll(remoteDir, 0755)
-	runGitCmd(t, remoteDir, "init", "--bare")
+	runGitCmd(t, remoteDir, "init", "--bare", "-b", "master")
 
 	// Clone1: Agent A
 	clone1Dir := filepath.Join(tmpDir, "clone1")
@@ -660,12 +660,12 @@ func TestSyncBranchIntegration_EndToEnd(t *testing.T) {
 
 	// Agent A creates issue
 	issue := &types.Issue{
-		Title:       "E2E test issue",
+		Title:     "E2E test issue",
-		Status:      types.StatusOpen,
+		Status:    types.StatusOpen,
-		Priority:    1,
+		Priority:  1,
-		IssueType:   types.TypeTask,
+		IssueType: types.TypeTask,
-		CreatedAt:   time.Now(),
+		CreatedAt: time.Now(),
-		UpdatedAt:   time.Now(),
+		UpdatedAt: time.Now(),
 	}
 	store1.CreateIssue(ctx, issue, "agent-a")
 	issueID := issue.ID
@@ -914,7 +914,7 @@ func TestSyncBranchMultipleConcurrentClones(t *testing.T) {
 	tmpDir := t.TempDir()
 	remoteDir := filepath.Join(tmpDir, "remote")
 	os.MkdirAll(remoteDir, 0755)
-	runGitCmd(t, remoteDir, "init", "--bare")
+	runGitCmd(t, remoteDir, "init", "--bare", "-b", "master")
 
 	syncBranch := "beads-sync"
 
@@ -1454,7 +1454,7 @@ func TestGitPushFromWorktree_FetchRebaseRetry(t *testing.T) {
 
 	// Create a "remote" bare repository
 	remoteDir := t.TempDir()
-	runGitCmd(t, remoteDir, "init", "--bare")
+	runGitCmd(t, remoteDir, "init", "--bare", "-b", "master")
 
 	// Create first clone (simulates another developer's clone)
 	clone1Dir := t.TempDir()
@@ -1524,7 +1524,7 @@ func TestGitPushFromWorktree_FetchRebaseRetry(t *testing.T) {
 
 	// Now try to push from worktree - this should trigger the fetch-rebase-retry logic
 	// because the remote has commits that the local worktree doesn't have
-	err := gitPushFromWorktree(ctx, worktreePath, "beads-sync")
+	err := gitPushFromWorktree(ctx, worktreePath, "beads-sync", "")
 	if err != nil {
 		t.Fatalf("gitPushFromWorktree failed: %v (expected fetch-rebase-retry to succeed)", err)
 	}

cmd/bd/delete_rpc_test.go

@@ -8,6 +8,7 @@ import (
 	"context"
 	"encoding/json"
 	"io"
+	"log/slog"
 	"os"
 	"path/filepath"
 	"strings"
@@ -897,11 +898,7 @@ func setupDaemonTestEnvForDelete(t *testing.T) (context.Context, context.CancelF
 
 	ctx, cancel := context.WithTimeout(context.Background(), 30*time.Second)
 
-	log := daemonLogger{
+	log := daemonLogger{logger: slog.New(slog.NewTextHandler(io.Discard, &slog.HandlerOptions{Level: slog.LevelInfo}))}
-		logFunc: func(format string, args ...interface{}) {
-			t.Logf("[daemon] "+format, args...)
-		},
-	}
 
 	server, _, err := startRPCServer(ctx, socketPath, testStore, tmpDir, testDBPath, log)
 	if err != nil {

cmd/bd/doctor/git_hygiene_test.go

@@ -12,7 +12,11 @@ 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)
+		// Fallback for platforms without /tmp (e.g. Windows).
+		dir, err = os.MkdirTemp("", prefix)
+		if err != nil {
+			t.Fatalf("failed to create temp dir: %v", err)
+		}
 	}
 	t.Cleanup(func() { _ = os.RemoveAll(dir) })
 	return dir

cmd/bd/doctor_repair_chaos_test.go

@@ -0,0 +1,125 @@
+//go:build chaos
+
+package main
+
+import (
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+)
+
+func TestDoctorRepair_CorruptDatabase_NotADatabase_RebuildFromJSONL(t *testing.T) {
+	bdExe := buildBDForTest(t)
+	ws := mkTmpDirInTmp(t, "bd-doctor-chaos-*")
+	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)
+	}
+
+	// Make the DB unreadable.
+	if err := os.WriteFile(dbPath, []byte("not a database"), 0644); err != nil {
+		t.Fatalf("corrupt db: %v", err)
+	}
+
+	if _, err := runBDSideDB(t, bdExe, ws, dbPath, "doctor", "--fix", "--yes"); err != nil {
+		t.Fatalf("bd doctor --fix failed: %v", err)
+	}
+
+	if out, err := runBDSideDB(t, bdExe, ws, dbPath, "doctor"); err != nil {
+		t.Fatalf("bd doctor after fix failed: %v\n%s", err, out)
+	}
+}
+
+func TestDoctorRepair_CorruptDatabase_NoJSONL_FixFails(t *testing.T) {
+	bdExe := buildBDForTest(t)
+	ws := mkTmpDirInTmp(t, "bd-doctor-chaos-nojsonl-*")
+	dbPath := filepath.Join(ws, ".beads", "beads.db")
+
+	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)
+	}
+
+	// Some workflows keep JSONL in sync automatically; force it to be missing.
+	_ = os.Remove(filepath.Join(ws, ".beads", "issues.jsonl"))
+	_ = os.Remove(filepath.Join(ws, ".beads", "beads.jsonl"))
+
+	// Corrupt without providing JSONL source-of-truth.
+	if err := os.Truncate(dbPath, 64); err != nil {
+		t.Fatalf("truncate db: %v", err)
+	}
+
+	out, err := runBDSideDB(t, bdExe, ws, dbPath, "doctor", "--fix", "--yes")
+	if err == nil {
+		t.Fatalf("expected bd doctor --fix to fail without JSONL")
+	}
+	if !strings.Contains(out, "cannot auto-recover") {
+		t.Fatalf("expected auto-recover error, got:\n%s", out)
+	}
+}
+
+func TestDoctorRepair_CorruptDatabase_BacksUpSidecars(t *testing.T) {
+	bdExe := buildBDForTest(t)
+	ws := mkTmpDirInTmp(t, "bd-doctor-chaos-sidecars-*")
+	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)
+	}
+
+	// Ensure sidecars exist so we can verify they get moved with the backup.
+	for _, suffix := range []string{"-wal", "-shm", "-journal"} {
+		if err := os.WriteFile(dbPath+suffix, []byte("x"), 0644); err != nil {
+			t.Fatalf("write sidecar %s: %v", suffix, err)
+		}
+	}
+	if err := os.Truncate(dbPath, 64); err != nil {
+		t.Fatalf("truncate db: %v", err)
+	}
+
+	if _, err := runBDSideDB(t, bdExe, ws, dbPath, "doctor", "--fix", "--yes"); err != nil {
+		t.Fatalf("bd doctor --fix failed: %v", err)
+	}
+
+	// Verify a backup exists, and at least one sidecar got moved.
+	entries, err := os.ReadDir(filepath.Join(ws, ".beads"))
+	if err != nil {
+		t.Fatalf("readdir: %v", err)
+	}
+	var backup string
+	for _, e := range entries {
+		if strings.Contains(e.Name(), ".corrupt.backup.db") {
+			backup = filepath.Join(ws, ".beads", e.Name())
+			break
+		}
+	}
+	if backup == "" {
+		t.Fatalf("expected backup db in .beads, found none")
+	}
+
+	wal := backup + "-wal"
+	if _, err := os.Stat(wal); err != nil {
+		// At minimum, the backup DB itself should exist; sidecar backup is best-effort.
+		if _, err2 := os.Stat(backup); err2 != nil {
+			t.Fatalf("backup db missing: %v", err2)
+		}
+	}
+}

cmd/bd/doctor_repair_test.go

@@ -31,7 +31,11 @@ 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)
+		// Fallback for platforms without /tmp (e.g. Windows).
+		dir, err = os.MkdirTemp("", prefix)
+		if err != nil {
+			t.Fatalf("failed to create temp dir: %v", err)
+		}
 	}
 	t.Cleanup(func() { _ = os.RemoveAll(dir) })
 	return dir

cmd/bd/git_sync_test.go

@@ -34,7 +34,7 @@ func TestGitPullSyncIntegration(t *testing.T) {
 	}
 
 	// Initialize remote git repo
-	runGitCmd(t, remoteDir, "init", "--bare")
+	runGitCmd(t, remoteDir, "init", "--bare", "-b", "master")
 
 	// Create "clone1" repository
 	clone1Dir := filepath.Join(tempDir, "clone1")

internal/beads/beads_hash_multiclone_test.go

@@ -177,7 +177,7 @@ func TestHashIDs_IdenticalContentDedup(t *testing.T) {
 func setupBareRepo(t *testing.T, tmpDir string) string {
 	t.Helper()
 	remoteDir := filepath.Join(tmpDir, "remote.git")
-	runCmd(t, tmpDir, "git", "init", "--bare", remoteDir)
+	runCmd(t, tmpDir, "git", "init", "--bare", "-b", "master", remoteDir)
 
 	tempClone := filepath.Join(tmpDir, "temp-init")
 	runCmd(t, tmpDir, "git", "clone", remoteDir, tempClone)