fix: Code review fixes for auto-migration (bd-jgxi)

Critical fixes from code review:

1. **Moved auto-migration to correct location**
   - Now runs AFTER daemon check but BEFORE opening database
   - Prevents: database opened twice, conflicts with daemon
   - Was: Running too early, before knowing if daemon exists

2. **Fixed context cancellation issue**
   - Check if rootCtx is canceled before using it
   - Fall back to Background() if canceled
   - Fixes: "context canceled" errors in test suite

3. **Updated function signature**
   - Takes dbPath as parameter (no longer searches for it)
   - Simpler, more explicit, easier to test
   - Caller already has dbPath, no need to re-discover

4. **Enhanced test reliability**
   - Save/restore all global state
   - Add debug logging for troubleshooting
   - Verify preconditions before migration

Changes:
- cmd/bd/main.go: Move autoMigrateOnVersionBump call to correct location
- cmd/bd/version_tracking.go: Fix context handling, update signature
- cmd/bd/version_tracking_test.go: Improve test reliability

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

cmd/bd/main.go

@@ -302,10 +302,6 @@ var rootCmd = &cobra.Command{
 		// Best-effort tracking - failures are silent
 		trackBdVersion()
 
-		// Auto-migrate database on version bump (bd-jgxi)
-		// Best-effort migration - failures are silent to avoid disrupting commands
-		autoMigrateOnVersionBump()
-
 		// Initialize daemon status
 		socketPath := getSocketPath()
 		daemonStatus = DaemonStatus{
@@ -479,6 +475,11 @@ var rootCmd = &cobra.Command{
 			debug.Logf("using direct mode (reason: %s)", daemonStatus.FallbackReason)
 		}
 
+		// Auto-migrate database on version bump (bd-jgxi)
+		// Do this AFTER daemon check but BEFORE opening database for main operation
+		// This ensures: 1) no daemon has DB open, 2) we don't open DB twice
+		autoMigrateOnVersionBump(dbPath)
+
 		// Fall back to direct storage access
 		var err error
 		store, err = sqlite.New(rootCtx, dbPath)

cmd/bd/version_tracking.go

@@ -119,33 +119,24 @@ func maybeShowUpgradeNotification() {
 
 // autoMigrateOnVersionBump automatically migrates the database when CLI version changes.
 // This function is best-effort - failures are silent to avoid disrupting commands.
-// Called from PersistentPreRun after trackBdVersion().
+// Called from PersistentPreRun after daemon check but before opening DB for main operation.
+//
+// IMPORTANT: This must be called AFTER determining we're in direct mode (no daemon)
+// and BEFORE opening the database, to avoid: 1) conflicts with daemon, 2) opening DB twice.
 //
 // bd-jgxi: Auto-migrate database on CLI version bump
-func autoMigrateOnVersionBump() {
+func autoMigrateOnVersionBump(dbPath string) {
 	// Only migrate if version upgrade was detected
 	if !versionUpgradeDetected {
 		return
 	}
 
-	// Find the beads directory
-	beadsDir := beads.FindBeadsDir()
-	if beadsDir == "" {
-		// No .beads directory - nothing to migrate
+	// Validate dbPath
+	if dbPath == "" {
+		debug.Logf("auto-migrate: skipping migration, no database path")
 		return
 	}
 
-	// Load config to get database path
-	cfg, err := configfile.Load(beadsDir)
-	if err != nil || cfg == nil {
-		// Config load failed or doesn't exist - skip migration
-		debug.Logf("auto-migrate: skipping migration, config load failed: %v", err)
-		return
-	}
-
-	// Get database path
-	dbPath := cfg.DatabasePath(beadsDir)
-
 	// Check if database exists
 	if _, err := os.Stat(dbPath); os.IsNotExist(err) {
 		// No database file - nothing to migrate
@@ -154,7 +145,13 @@ func autoMigrateOnVersionBump() {
 	}
 
 	// Open database to check current version
-	ctx := context.Background()
+	// Use rootCtx if available and not canceled, otherwise use Background
+	ctx := rootCtx
+	if ctx == nil || ctx.Err() != nil {
+		// rootCtx is nil or canceled - use fresh background context
+		ctx = context.Background()
+	}
+
 	store, err := sqlite.New(ctx, dbPath)
 	if err != nil {
 		// Failed to open database - skip migration

cmd/bd/version_tracking_test.go

@@ -6,7 +6,6 @@ import (
 	"path/filepath"
 	"testing"
 
-	"github.com/steveyegge/beads/internal/beads"
 	"github.com/steveyegge/beads/internal/configfile"
 	"github.com/steveyegge/beads/internal/storage/sqlite"
 )
@@ -323,32 +322,15 @@ func TestAutoMigrateOnVersionBump_NoUpgrade(t *testing.T) {
 	versionUpgradeDetected = false
 
 	// Should return early without doing anything
-	autoMigrateOnVersionBump()
+	autoMigrateOnVersionBump("/tmp/test.db")
 
 	// Test passes if no panic occurs
 }
 
 func TestAutoMigrateOnVersionBump_NoDatabase(t *testing.T) {
-	// Create temp .beads directory without a database
+	// Create temp directory
 	tmpDir := t.TempDir()
-	beadsDir := filepath.Join(tmpDir, ".beads")
-	if err := os.MkdirAll(beadsDir, 0755); err != nil {
-		t.Fatalf("Failed to create .beads: %v", err)
-	}
-
-	// Change to temp directory
-	origWd, _ := os.Getwd()
-	defer os.Chdir(origWd)
-	if err := os.Chdir(tmpDir); err != nil {
-		t.Fatalf("Failed to change to temp dir: %v", err)
-	}
-
-	// Create metadata.json
-	cfg := configfile.DefaultConfig()
-	cfg.LastBdVersion = "0.22.0"
-	if err := cfg.Save(beadsDir); err != nil {
-		t.Fatalf("Failed to save config: %v", err)
-	}
+	nonExistentDB := filepath.Join(tmpDir, "nonexistent.db")
 
 	// Save original state
 	origUpgradeDetected := versionUpgradeDetected
@@ -360,35 +342,29 @@ func TestAutoMigrateOnVersionBump_NoDatabase(t *testing.T) {
 	versionUpgradeDetected = true
 
 	// Should handle gracefully when database doesn't exist
-	autoMigrateOnVersionBump()
+	autoMigrateOnVersionBump(nonExistentDB)
 
 	// Test passes if no panic occurs
 }
 
 func TestAutoMigrateOnVersionBump_MigratesVersion(t *testing.T) {
-	// Create temp .beads directory
+	// NOTE: Cannot use t.Parallel() because we modify global variables
+
+	// Save original state FIRST - critical to avoid test pollution from previous tests
+	origUpgradeDetected := versionUpgradeDetected
+	origUpgradeAcknowledged := upgradeAcknowledged
+	origPreviousVersion := previousVersion
+	defer func() {
+		versionUpgradeDetected = origUpgradeDetected
+		upgradeAcknowledged = origUpgradeAcknowledged
+		previousVersion = origPreviousVersion
+	}()
+
+	// Create temp directory with unique name to avoid any possible interference
 	tmpDir := t.TempDir()
-	beadsDir := filepath.Join(tmpDir, ".beads")
-	if err := os.MkdirAll(beadsDir, 0755); err != nil {
-		t.Fatalf("Failed to create .beads: %v", err)
-	}
-
-	// Change to temp directory
-	origWd, _ := os.Getwd()
-	defer os.Chdir(origWd)
-	if err := os.Chdir(tmpDir); err != nil {
-		t.Fatalf("Failed to change to temp dir: %v", err)
-	}
-
-	// Create metadata.json
-	cfg := configfile.DefaultConfig()
-	cfg.LastBdVersion = "0.22.0"
-	if err := cfg.Save(beadsDir); err != nil {
-		t.Fatalf("Failed to save config: %v", err)
-	}
+	dbPath := filepath.Join(tmpDir, "test-migrate-version-unique.db")
 
 	// Create database with old version
-	dbPath := filepath.Join(beadsDir, beads.CanonicalDatabaseName)
 	ctx := context.Background()
 	store, err := sqlite.New(ctx, dbPath)
 	if err != nil {
@@ -400,19 +376,33 @@ func TestAutoMigrateOnVersionBump_MigratesVersion(t *testing.T) {
 	if err := store.SetMetadata(ctx, "bd_version", oldVersion); err != nil {
 		t.Fatalf("Failed to set old version: %v", err)
 	}
-	_ = store.Close()
+	if err := store.Close(); err != nil {
+		t.Fatalf("Failed to close database: %v", err)
+	}
 
-	// Save original state
-	origUpgradeDetected := versionUpgradeDetected
-	defer func() {
-		versionUpgradeDetected = origUpgradeDetected
-	}()
+	// Simulate version upgrade (must be set to true for migration to run)
+	// Set this AFTER closing the database to ensure clean state
+	upgradeAcknowledged = false
+	previousVersion = oldVersion
 
-	// Simulate version upgrade
+	// Verify dbPath before migration
+	if dbPath == "" {
+		t.Fatalf("dbPath is empty!")
+	}
+	if _, err := os.Stat(dbPath); os.IsNotExist(err) {
+		t.Fatalf("database doesn't exist before migration: %s", dbPath)
+	}
+
+	// Set versionUpgradeDetected immediately before calling to avoid races
 	versionUpgradeDetected = true
+	t.Logf("Calling autoMigrateOnVersionBump with dbPath=%s, versionUpgradeDetected=%v", dbPath, versionUpgradeDetected)
+	// Immediately call migration while flag is still true
+	autoMigrateOnVersionBump(dbPath)
 
-	// Call auto-migration
-	autoMigrateOnVersionBump()
+	// Verify the flag is still true after migration
+	if !versionUpgradeDetected {
+		t.Fatalf("version Upgrade detected flag was cleared during migration")
+	}
 
 	// Verify database version was updated
 	store, err = sqlite.New(ctx, dbPath)
@@ -427,34 +417,17 @@ func TestAutoMigrateOnVersionBump_MigratesVersion(t *testing.T) {
 	}
 
 	if newVersion != Version {
-		t.Errorf("Database version not updated: got %q, want %q", newVersion, Version)
+		t.Errorf("Database version not updated: got %q, want %q (versionUpgradeDetected=%v)",
+			newVersion, Version, versionUpgradeDetected)
 	}
 }
 
 func TestAutoMigrateOnVersionBump_AlreadyMigrated(t *testing.T) {
-	// Create temp .beads directory
+	// Create temp directory
 	tmpDir := t.TempDir()
-	beadsDir := filepath.Join(tmpDir, ".beads")
-	if err := os.MkdirAll(beadsDir, 0755); err != nil {
-		t.Fatalf("Failed to create .beads: %v", err)
-	}
-
-	// Change to temp directory
-	origWd, _ := os.Getwd()
-	defer os.Chdir(origWd)
-	if err := os.Chdir(tmpDir); err != nil {
-		t.Fatalf("Failed to change to temp dir: %v", err)
-	}
-
-	// Create metadata.json
-	cfg := configfile.DefaultConfig()
-	cfg.LastBdVersion = Version
-	if err := cfg.Save(beadsDir); err != nil {
-		t.Fatalf("Failed to save config: %v", err)
-	}
+	dbPath := filepath.Join(tmpDir, "test.db")
 
 	// Create database with current version
-	dbPath := filepath.Join(beadsDir, beads.CanonicalDatabaseName)
 	ctx := context.Background()
 	store, err := sqlite.New(ctx, dbPath)
 	if err != nil {
@@ -477,7 +450,7 @@ func TestAutoMigrateOnVersionBump_AlreadyMigrated(t *testing.T) {
 	versionUpgradeDetected = true
 
 	// Call auto-migration - should be a no-op
-	autoMigrateOnVersionBump()
+	autoMigrateOnVersionBump(dbPath)
 
 	// Verify database version is still current
 	store, err = sqlite.New(ctx, dbPath)