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

@@ -30,36 +30,36 @@ func TestDaemonAutoImportAfterGitPull(t *testing.T) {
 		t.Fatal(err)
 	}
 	defer os.RemoveAll(tempDir)
-	
+
 	// Create "remote" repository
 	remoteDir := filepath.Join(tempDir, "remote")
 	if err := os.MkdirAll(remoteDir, 0750); err != nil {
 		t.Fatalf("Failed to create remote dir: %v", err)
 	}
-	
+
 	// 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")
 	runGitCmd(t, tempDir, "clone", remoteDir, clone1Dir)
 	configureGit(t, clone1Dir)
-	
+
 	// Initialize beads in clone1
 	clone1BeadsDir := filepath.Join(clone1Dir, ".beads")
 	if err := os.MkdirAll(clone1BeadsDir, 0750); err != nil {
 		t.Fatalf("Failed to create .beads dir: %v", err)
 	}
-	
+
 	clone1DBPath := filepath.Join(clone1BeadsDir, "test.db")
 	clone1Store := newTestStore(t, clone1DBPath)
 	defer clone1Store.Close()
-	
+
 	ctx := context.Background()
 	if err := clone1Store.SetMetadata(ctx, "issue_prefix", "test"); err != nil {
 		t.Fatalf("Failed to set prefix: %v", err)
 	}
-	
+
 	// Create an open issue in clone1
 	issue := &types.Issue{
 		Title:     "Test daemon auto-import",
@@ -73,39 +73,39 @@ func TestDaemonAutoImportAfterGitPull(t *testing.T) {
 		t.Fatalf("Failed to create issue: %v", err)
 	}
 	issueID := issue.ID
-	
+
 	// Export to JSONL
 	jsonlPath := filepath.Join(clone1BeadsDir, "issues.jsonl")
 	if err := exportIssuesToJSONL(ctx, clone1Store, jsonlPath); err != nil {
 		t.Fatalf("Failed to export: %v", err)
 	}
-	
+
 	// Commit and push from clone1
 	runGitCmd(t, clone1Dir, "add", ".beads")
 	runGitCmd(t, clone1Dir, "commit", "-m", "Add test issue")
 	runGitCmd(t, clone1Dir, "push", "origin", "master")
-	
+
 	// Create "clone2" repository (Agent B)
 	clone2Dir := filepath.Join(tempDir, "clone2")
 	runGitCmd(t, tempDir, "clone", remoteDir, clone2Dir)
 	configureGit(t, clone2Dir)
-	
+
 	// Initialize empty database in clone2
 	clone2BeadsDir := filepath.Join(clone2Dir, ".beads")
 	clone2DBPath := filepath.Join(clone2BeadsDir, "test.db")
 	clone2Store := newTestStore(t, clone2DBPath)
 	defer clone2Store.Close()
-	
+
 	if err := clone2Store.SetMetadata(ctx, "issue_prefix", "test"); err != nil {
 		t.Fatalf("Failed to set prefix: %v", err)
 	}
-	
+
 	// Import initial JSONL in clone2
 	clone2JSONLPath := filepath.Join(clone2BeadsDir, "issues.jsonl")
 	if err := importJSONLToStore(ctx, clone2Store, clone2DBPath, clone2JSONLPath); err != nil {
 		t.Fatalf("Failed to import: %v", err)
 	}
-	
+
 	// Verify issue exists in clone2
 	initialIssue, err := clone2Store.GetIssue(ctx, issueID)
 	if err != nil {
@@ -114,27 +114,27 @@ func TestDaemonAutoImportAfterGitPull(t *testing.T) {
 	if initialIssue.Status != types.StatusOpen {
 		t.Errorf("Expected status open, got %s", initialIssue.Status)
 	}
-	
+
 	// NOW THE CRITICAL TEST: Agent A closes the issue and pushes
 	t.Run("DaemonAutoImportsAfterGitPull", func(t *testing.T) {
 		// Agent A closes the issue
 		if err := clone1Store.CloseIssue(ctx, issueID, "Completed", "agent-a"); err != nil {
 			t.Fatalf("Failed to close issue: %v", err)
 		}
-		
+
 		// Agent A exports to JSONL
 		if err := exportIssuesToJSONL(ctx, clone1Store, jsonlPath); err != nil {
 			t.Fatalf("Failed to export after close: %v", err)
 		}
-		
+
 		// Agent A commits and pushes
 		runGitCmd(t, clone1Dir, "add", ".beads/issues.jsonl")
 		runGitCmd(t, clone1Dir, "commit", "-m", "Close issue")
 		runGitCmd(t, clone1Dir, "push", "origin", "master")
-		
+
 		// Agent B does git pull (updates JSONL on disk)
 		runGitCmd(t, clone2Dir, "pull")
-		
+
 		// Wait for filesystem to settle after git operations
 		// Windows has lower filesystem timestamp precision (typically 100ms)
 		// and file I/O may be slower, so we need a longer delay
@@ -143,23 +143,23 @@ func TestDaemonAutoImportAfterGitPull(t *testing.T) {
 		} else {
 			time.Sleep(50 * time.Millisecond)
 		}
-		
+
 		// Start daemon server in clone2
 		socketPath := filepath.Join(clone2BeadsDir, "bd.sock")
 		os.Remove(socketPath) // Ensure clean state
-		
+
 		server := rpc.NewServer(socketPath, clone2Store, clone2Dir, clone2DBPath)
-		
+
 		// Start server in background
 		serverCtx, serverCancel := context.WithCancel(context.Background())
 		defer serverCancel()
-		
+
 		go func() {
 			if err := server.Start(serverCtx); err != nil {
 				t.Logf("Server error: %v", err)
 			}
 		}()
-		
+
 		// Wait for server to be ready
 		for i := 0; i < 50; i++ {
 			time.Sleep(10 * time.Millisecond)
@@ -167,7 +167,7 @@ func TestDaemonAutoImportAfterGitPull(t *testing.T) {
 				break
 			}
 		}
-		
+
 		// Simulate a daemon request (like "bd show <issue>")
 		// The daemon should auto-import the updated JSONL before responding
 		client, err := rpc.TryConnect(socketPath)
@@ -178,15 +178,15 @@ func TestDaemonAutoImportAfterGitPull(t *testing.T) {
 			t.Fatal("Client is nil")
 		}
 		defer client.Close()
-		
+
 		client.SetDatabasePath(clone2DBPath) // Route to correct database
-		
+
 		// Make a request that triggers auto-import check
 		resp, err := client.Execute("show", map[string]string{"id": issueID})
 		if err != nil {
 			t.Fatalf("Failed to get issue from daemon: %v", err)
 		}
-		
+
 		// Parse response
 		var issue types.Issue
 		issueJSON, err := json.Marshal(resp.Data)
@@ -196,25 +196,25 @@ func TestDaemonAutoImportAfterGitPull(t *testing.T) {
 		if err := json.Unmarshal(issueJSON, &issue); err != nil {
 			t.Fatalf("Failed to unmarshal issue: %v", err)
 		}
-		
+
 		status := issue.Status
-		
+
 		// CRITICAL ASSERTION: Daemon should return CLOSED status from JSONL
 		// not stale OPEN status from SQLite
 		if status != types.StatusClosed {
 			t.Errorf("DAEMON AUTO-IMPORT FAILED: Expected status 'closed' but got '%s'", status)
 			t.Errorf("This means daemon is serving stale SQLite data instead of auto-importing JSONL")
-			
+
 			// Double-check JSONL has correct status
 			jsonlData, _ := os.ReadFile(clone2JSONLPath)
 			t.Logf("JSONL content: %s", string(jsonlData))
-			
+
 			// Double-check what's in SQLite
 			directIssue, _ := clone2Store.GetIssue(ctx, issueID)
 			t.Logf("SQLite status: %s", directIssue.Status)
 		}
 	})
-	
+
 	// Additional test: Verify multiple rapid changes
 	t.Run("DaemonHandlesRapidUpdates", func(t *testing.T) {
 		// Agent A updates priority
@@ -223,18 +223,18 @@ func TestDaemonAutoImportAfterGitPull(t *testing.T) {
 		}, "agent-a"); err != nil {
 			t.Fatalf("Failed to update priority: %v", err)
 		}
-		
+
 		if err := exportIssuesToJSONL(ctx, clone1Store, jsonlPath); err != nil {
 			t.Fatalf("Failed to export: %v", err)
 		}
-		
+
 		runGitCmd(t, clone1Dir, "add", ".beads/issues.jsonl")
 		runGitCmd(t, clone1Dir, "commit", "-m", "Update priority")
 		runGitCmd(t, clone1Dir, "push", "origin", "master")
-		
+
 		// Agent B pulls
 		runGitCmd(t, clone2Dir, "pull")
-		
+
 		// Query via daemon - should see priority 0
 		// (Execute forces auto-import synchronously)
 		socketPath := filepath.Join(clone2BeadsDir, "bd.sock")
@@ -243,18 +243,18 @@ func TestDaemonAutoImportAfterGitPull(t *testing.T) {
 			t.Fatalf("Failed to connect to daemon: %v", err)
 		}
 		defer client.Close()
-		
+
 		client.SetDatabasePath(clone2DBPath) // Route to correct database
-		
+
 		resp, err := client.Execute("show", map[string]string{"id": issueID})
 		if err != nil {
 			t.Fatalf("Failed to get issue from daemon: %v", err)
 		}
-		
+
 		var issue types.Issue
 		issueJSON, _ := json.Marshal(resp.Data)
 		json.Unmarshal(issueJSON, &issue)
-		
+
 		if issue.Priority != 0 {
 			t.Errorf("Expected priority 0 after auto-import, got %d", issue.Priority)
 		}
@@ -273,23 +273,23 @@ func TestDaemonAutoImportDataCorruption(t *testing.T) {
 		t.Fatal(err)
 	}
 	defer os.RemoveAll(tempDir)
-	
+
 	// 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)
 	configureGit(t, clone1Dir)
-	
+
 	clone2Dir := filepath.Join(tempDir, "clone2")
 	runGitCmd(t, tempDir, "clone", remoteDir, clone2Dir)
 	configureGit(t, clone2Dir)
-	
+
 	// Initialize beads in both clones
 	ctx := context.Background()
-	
+
 	// Clone1 setup
 	clone1BeadsDir := filepath.Join(clone1Dir, ".beads")
 	os.MkdirAll(clone1BeadsDir, 0750)
@@ -297,7 +297,7 @@ func TestDaemonAutoImportDataCorruption(t *testing.T) {
 	clone1Store := newTestStore(t, clone1DBPath)
 	defer clone1Store.Close()
 	clone1Store.SetMetadata(ctx, "issue_prefix", "test")
-	
+
 	// Clone2 setup
 	clone2BeadsDir := filepath.Join(clone2Dir, ".beads")
 	os.MkdirAll(clone2BeadsDir, 0750)
@@ -305,7 +305,7 @@ func TestDaemonAutoImportDataCorruption(t *testing.T) {
 	clone2Store := newTestStore(t, clone2DBPath)
 	defer clone2Store.Close()
 	clone2Store.SetMetadata(ctx, "issue_prefix", "test")
-	
+
 	// Agent A creates issue and pushes
 	issue2 := &types.Issue{
 		Title:     "Shared issue",
@@ -317,18 +317,18 @@ func TestDaemonAutoImportDataCorruption(t *testing.T) {
 	}
 	clone1Store.CreateIssue(ctx, issue2, "agent-a")
 	issueID := issue2.ID
-	
+
 	clone1JSONLPath := filepath.Join(clone1BeadsDir, "issues.jsonl")
 	exportIssuesToJSONL(ctx, clone1Store, clone1JSONLPath)
 	runGitCmd(t, clone1Dir, "add", ".beads")
 	runGitCmd(t, clone1Dir, "commit", "-m", "Initial issue")
 	runGitCmd(t, clone1Dir, "push", "origin", "master")
-	
+
 	// Agent B pulls and imports
 	runGitCmd(t, clone2Dir, "pull")
 	clone2JSONLPath := filepath.Join(clone2BeadsDir, "issues.jsonl")
 	importJSONLToStore(ctx, clone2Store, clone2DBPath, clone2JSONLPath)
-	
+
 	// THE CORRUPTION SCENARIO:
 	// 1. Agent A closes the issue and pushes
 	clone1Store.CloseIssue(ctx, issueID, "Done", "agent-a")
@@ -336,31 +336,31 @@ func TestDaemonAutoImportDataCorruption(t *testing.T) {
 	runGitCmd(t, clone1Dir, "add", ".beads/issues.jsonl")
 	runGitCmd(t, clone1Dir, "commit", "-m", "Close issue")
 	runGitCmd(t, clone1Dir, "push", "origin", "master")
-	
+
 	// 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
-	
+
 	// Start daemon in clone2
 	socketPath := filepath.Join(clone2BeadsDir, "bd.sock")
 	os.Remove(socketPath)
-	
+
 	server := rpc.NewServer(socketPath, clone2Store, clone2Dir, clone2DBPath)
-	
+
 	serverCtx, serverCancel := context.WithCancel(context.Background())
 	defer serverCancel()
-	
+
 	go func() {
 		if err := server.Start(serverCtx); err != nil {
 			t.Logf("Server error: %v", err)
 		}
 	}()
-	
+
 	// Wait for server
 	for i := 0; i < 50; i++ {
 		time.Sleep(10 * time.Millisecond)
@@ -368,43 +368,43 @@ func TestDaemonAutoImportDataCorruption(t *testing.T) {
 			break
 		}
 	}
-	
+
 	// Trigger daemon operation (should auto-import first)
 	client, err := rpc.TryConnect(socketPath)
 	if err != nil {
 		t.Fatalf("Failed to connect: %v", err)
 	}
 	defer client.Close()
-	
+
 	client.SetDatabasePath(clone2DBPath)
-	
+
 	resp, err := client.Execute("show", map[string]string{"id": issueID})
 	if err != nil {
 		t.Fatalf("Failed to get issue: %v", err)
 	}
-	
+
 	var issue types.Issue
 	issueJSON, _ := json.Marshal(resp.Data)
 	json.Unmarshal(issueJSON, &issue)
-	
+
 	status := issue.Status
-	
+
 	// If daemon didn't auto-import, this would be "open" (stale)
 	// With the fix, it should be "closed" (fresh from JSONL)
 	if status != types.StatusClosed {
 		t.Errorf("DATA CORRUPTION DETECTED: Daemon has stale status '%s' instead of 'closed'", status)
 		t.Error("If daemon exports this stale data, it will overwrite Agent A's changes on next push")
 	}
-	
+
 	// Now simulate daemon export (which happens on timer)
 	// With auto-import working, this export should have fresh data
 	exportIssuesToJSONL(ctx, clone2Store, clone2JSONLPath)
-	
+
 	// Read back JSONL to verify it has correct status
 	data, _ := os.ReadFile(clone2JSONLPath)
 	var exportedIssue types.Issue
 	json.NewDecoder(bytes.NewReader(data)).Decode(&exportedIssue)
-	
+
 	if exportedIssue.Status != types.StatusClosed {
 		t.Errorf("CORRUPTION: Exported JSONL has wrong status '%s', would overwrite remote", exportedIssue.Status)
 	}

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",
-		Status:      types.StatusOpen,
-		Priority:    1,
-		IssueType:   types.TypeTask,
-		CreatedAt:   time.Now(),
-		UpdatedAt:   time.Now(),
+		Title:     "Test issue",
+		Status:    types.StatusOpen,
+		Priority:  1,
+		IssueType: types.TypeTask,
+		CreatedAt: 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",
-		Status:      types.StatusOpen,
-		Priority:    1,
-		IssueType:   types.TypeTask,
-		CreatedAt:   time.Now(),
-		UpdatedAt:   time.Now(),
+		Title:     "Test sync branch issue",
+		Status:    types.StatusOpen,
+		Priority:  1,
+		IssueType: types.TypeTask,
+		CreatedAt: 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",
-		Status:      types.StatusOpen,
-		Priority:    1,
-		IssueType:   types.TypeTask,
-		CreatedAt:   time.Now(),
-		UpdatedAt:   time.Now(),
+		Title:     "Env override issue",
+		Status:    types.StatusOpen,
+		Priority:  1,
+		IssueType: types.TypeTask,
+		CreatedAt: 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",
-		Status:      types.StatusOpen,
-		Priority:    1,
-		IssueType:   types.TypeTask,
-		CreatedAt:   time.Now(),
-		UpdatedAt:   time.Now(),
+		Title:     "Test issue",
+		Status:    types.StatusOpen,
+		Priority:  1,
+		IssueType: types.TypeTask,
+		CreatedAt: 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",
-		Status:      types.StatusOpen,
-		Priority:    1,
-		IssueType:   types.TypeTask,
-		CreatedAt:   time.Now(),
-		UpdatedAt:   time.Now(),
+		Title:     "Test issue",
+		Status:    types.StatusOpen,
+		Priority:  1,
+		IssueType: types.TypeTask,
+		CreatedAt: 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",
-		Status:      types.StatusOpen,
-		Priority:    1,
-		IssueType:   types.TypeTask,
-		CreatedAt:   time.Now(),
-		UpdatedAt:   time.Now(),
+		Title:     "Test sync pull issue",
+		Status:    types.StatusOpen,
+		Priority:  1,
+		IssueType: types.TypeTask,
+		CreatedAt: 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",
-		Status:      types.StatusOpen,
-		Priority:    1,
-		IssueType:   types.TypeTask,
-		CreatedAt:   time.Now(),
-		UpdatedAt:   time.Now(),
+		Title:     "E2E test issue",
+		Status:    types.StatusOpen,
+		Priority:  1,
+		IssueType: types.TypeTask,
+		CreatedAt: 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{
-		logFunc: func(format string, args ...interface{}) {
-			t.Logf("[daemon] "+format, args...)
-		},
-	}
+	log := daemonLogger{logger: slog.New(slog.NewTextHandler(io.Discard, &slog.HandlerOptions{Level: slog.LevelInfo}))}
 
 	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

@@ -26,36 +26,36 @@ func TestGitPullSyncIntegration(t *testing.T) {
 
 	// Create temp directory for test repositories
 	tempDir := t.TempDir()
-	
+
 	// Create "remote" repository
 	remoteDir := filepath.Join(tempDir, "remote")
 	if err := os.MkdirAll(remoteDir, 0750); err != nil {
 		t.Fatalf("Failed to create remote dir: %v", err)
 	}
-	
+
 	// Initialize remote git repo
-	runGitCmd(t, remoteDir, "init", "--bare")
-	
+	runGitCmd(t, remoteDir, "init", "--bare", "-b", "master")
+
 	// Create "clone1" repository
 	clone1Dir := filepath.Join(tempDir, "clone1")
 	runGitCmd(t, tempDir, "clone", remoteDir, clone1Dir)
 	configureGit(t, clone1Dir)
-	
+
 	// Initialize beads in clone1
 	clone1BeadsDir := filepath.Join(clone1Dir, ".beads")
 	if err := os.MkdirAll(clone1BeadsDir, 0750); err != nil {
 		t.Fatalf("Failed to create .beads dir: %v", err)
 	}
-	
+
 	clone1DBPath := filepath.Join(clone1BeadsDir, "test.db")
 	clone1Store := newTestStore(t, clone1DBPath)
 	defer clone1Store.Close()
-	
+
 	ctx := context.Background()
 	if err := clone1Store.SetMetadata(ctx, "issue_prefix", "test"); err != nil {
 		t.Fatalf("Failed to set prefix: %v", err)
 	}
-	
+
 	// Create and close an issue in clone1
 	issue := &types.Issue{
 		Title:     "Test sync issue",
@@ -69,80 +69,80 @@ func TestGitPullSyncIntegration(t *testing.T) {
 		t.Fatalf("Failed to create issue: %v", err)
 	}
 	issueID := issue.ID
-	
+
 	// Close the issue
 	if err := clone1Store.CloseIssue(ctx, issueID, "Test completed", "test-user"); err != nil {
 		t.Fatalf("Failed to close issue: %v", err)
 	}
-	
+
 	// Export to JSONL
 	jsonlPath := filepath.Join(clone1BeadsDir, "issues.jsonl")
 	if err := exportIssuesToJSONL(ctx, clone1Store, jsonlPath); err != nil {
 		t.Fatalf("Failed to export: %v", err)
 	}
-	
+
 	// Commit and push from clone1
 	runGitCmd(t, clone1Dir, "add", ".beads")
 	runGitCmd(t, clone1Dir, "commit", "-m", "Add closed issue")
 	runGitCmd(t, clone1Dir, "push", "origin", "master")
-	
+
 	// Create "clone2" repository
 	clone2Dir := filepath.Join(tempDir, "clone2")
 	runGitCmd(t, tempDir, "clone", remoteDir, clone2Dir)
 	configureGit(t, clone2Dir)
-	
+
 	// Initialize empty database in clone2
 	clone2BeadsDir := filepath.Join(clone2Dir, ".beads")
 	clone2DBPath := filepath.Join(clone2BeadsDir, "test.db")
 	clone2Store := newTestStore(t, clone2DBPath)
 	defer clone2Store.Close()
-	
+
 	if err := clone2Store.SetMetadata(ctx, "issue_prefix", "test"); err != nil {
 		t.Fatalf("Failed to set prefix: %v", err)
 	}
-	
+
 	// Import the existing JSONL (simulating initial sync)
 	clone2JSONLPath := filepath.Join(clone2BeadsDir, "issues.jsonl")
 	if err := importJSONLToStore(ctx, clone2Store, clone2DBPath, clone2JSONLPath); err != nil {
 		t.Fatalf("Failed to import: %v", err)
 	}
-	
+
 	// Verify issue exists and is closed
 	verifyIssueClosed(t, clone2Store, issueID)
-	
+
 	// Note: We don't commit in clone2 - it stays clean as a read-only consumer
-	
+
 	// Now test git pull scenario: Clone1 makes a change (update priority)
 	if err := clone1Store.UpdateIssue(ctx, issueID, map[string]interface{}{
 		"priority": 0,
 	}, "test-user"); err != nil {
 		t.Fatalf("Failed to update issue: %v", err)
 	}
-	
+
 	if err := exportIssuesToJSONL(ctx, clone1Store, jsonlPath); err != nil {
 		t.Fatalf("Failed to export after update: %v", err)
 	}
-	
+
 	runGitCmd(t, clone1Dir, "add", ".beads/issues.jsonl")
 	runGitCmd(t, clone1Dir, "commit", "-m", "Update priority")
 	runGitCmd(t, clone1Dir, "push", "origin", "master")
-	
+
 	// Clone2 pulls the change
 	runGitCmd(t, clone2Dir, "pull")
-	
+
 	// Test auto-import in non-daemon mode
 	t.Run("NonDaemonAutoImport", func(t *testing.T) {
 		// Use a temporary local store for this test
 		localStore := newTestStore(t, clone2DBPath)
 		defer localStore.Close()
-		
+
 		// Manually import to simulate auto-import behavior
 		startTime := time.Now()
 		if err := importJSONLToStore(ctx, localStore, clone2DBPath, clone2JSONLPath); err != nil {
 			t.Fatalf("Failed to auto-import: %v", err)
 		}
 		elapsed := time.Since(startTime)
-		
+
 		// Verify priority was updated
 		issue, err := localStore.GetIssue(ctx, issueID)
 		if err != nil {
@@ -151,13 +151,13 @@ func TestGitPullSyncIntegration(t *testing.T) {
 		if issue.Priority != 0 {
 			t.Errorf("Expected priority 0 after auto-import, got %d", issue.Priority)
 		}
-		
+
 		// Verify performance: import should be fast
 		if elapsed > 100*time.Millisecond {
 			t.Logf("Info: import took %v", elapsed)
 		}
 	})
-	
+
 	// Test bd sync --import-only command
 	t.Run("BdSyncCommand", func(t *testing.T) {
 		// Make another change in clone1 (change priority back to 1)
@@ -166,27 +166,27 @@ func TestGitPullSyncIntegration(t *testing.T) {
 		}, "test-user"); err != nil {
 			t.Fatalf("Failed to update issue: %v", err)
 		}
-		
+
 		if err := exportIssuesToJSONL(ctx, clone1Store, jsonlPath); err != nil {
 			t.Fatalf("Failed to export: %v", err)
 		}
-		
+
 		runGitCmd(t, clone1Dir, "add", ".beads/issues.jsonl")
 		runGitCmd(t, clone1Dir, "commit", "-m", "Update priority")
 		runGitCmd(t, clone1Dir, "push", "origin", "master")
-		
+
 		// Clone2 pulls
 		runGitCmd(t, clone2Dir, "pull")
-		
+
 		// Use a fresh store for import
 		syncStore := newTestStore(t, clone2DBPath)
 		defer syncStore.Close()
-		
+
 		// Manually trigger import via in-process equivalent
 		if err := importJSONLToStore(ctx, syncStore, clone2DBPath, clone2JSONLPath); err != nil {
 			t.Fatalf("Failed to import via sync: %v", err)
 		}
-		
+
 		// Verify priority was updated back to 1
 		issue, err := syncStore.GetIssue(ctx, issueID)
 		if err != nil {
@@ -214,7 +214,7 @@ 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
@@ -233,7 +233,7 @@ func exportIssuesToJSONL(ctx context.Context, store *sqlite.SQLiteStorage, jsonl
 	if err != nil {
 		return err
 	}
-	
+
 	// Populate dependencies
 	allDeps, err := store.GetAllDependencyRecords(ctx)
 	if err != nil {
@@ -244,20 +244,20 @@ func exportIssuesToJSONL(ctx context.Context, store *sqlite.SQLiteStorage, jsonl
 		labels, _ := store.GetLabels(ctx, issue.ID)
 		issue.Labels = labels
 	}
-	
+
 	f, err := os.Create(jsonlPath)
 	if err != nil {
 		return err
 	}
 	defer f.Close()
-	
+
 	encoder := json.NewEncoder(f)
 	for _, issue := range issues {
 		if err := encoder.Encode(issue); err != nil {
 			return err
 		}
 	}
-	
+
 	return nil
 }
 
@@ -266,7 +266,7 @@ func importJSONLToStore(ctx context.Context, store *sqlite.SQLiteStorage, dbPath
 	if err != nil {
 		return err
 	}
-	
+
 	// Use the autoimport package's AutoImportIfNewer function
 	// For testing, we'll directly parse and import
 	var issues []*types.Issue
@@ -278,7 +278,7 @@ func importJSONLToStore(ctx context.Context, store *sqlite.SQLiteStorage, dbPath
 		}
 		issues = append(issues, &issue)
 	}
-	
+
 	// Import each issue
 	for _, issue := range issues {
 		existing, _ := store.GetIssue(ctx, issue.ID)
@@ -298,12 +298,12 @@ 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
 }