Fix Dolt backend init/daemon/doctor; prevent accidental SQLite artifacts; add integration tests; clean up lint (#1218)

* /{cmd,internal}: get dolt backend init working and allow issue creation

* /{website,internal,docs,cmd}: integration tests and more split backend fixes

* /{cmd,internal}: fix lint issues

* /cmd/bd/doctor/integrity.go: fix unable to query issues bug with dolt backend

* /cmd/bd/daemon.go: remove debug logging

internal/configfile/configfile.go

@@ -5,6 +5,7 @@ import (
 	"fmt"
 	"os"
 	"path/filepath"
+	"strings"
 )
 
 const ConfigFileName = "metadata.json"
@@ -37,7 +38,7 @@ func ConfigPath(beadsDir string) string {
 
 func Load(beadsDir string) (*Config, error) {
 	configPath := ConfigPath(beadsDir)
-	
+
 	data, err := os.ReadFile(configPath) // #nosec G304 - controlled path from config
 	if os.IsNotExist(err) {
 		// Try legacy config.json location (migration path)
@@ -49,52 +50,79 @@ func Load(beadsDir string) (*Config, error) {
 		if err != nil {
 			return nil, fmt.Errorf("reading legacy config: %w", err)
 		}
-		
+
 		// Migrate: parse legacy config, save as metadata.json, remove old file
 		var cfg Config
 		if err := json.Unmarshal(data, &cfg); err != nil {
 			return nil, fmt.Errorf("parsing legacy config: %w", err)
 		}
-		
+
 		// Save to new location
 		if err := cfg.Save(beadsDir); err != nil {
 			return nil, fmt.Errorf("migrating config to metadata.json: %w", err)
 		}
-		
+
 		// Remove legacy file (best effort)
 		_ = os.Remove(legacyPath)
-		
+
 		return &cfg, nil
 	}
 	if err != nil {
 		return nil, fmt.Errorf("reading config: %w", err)
 	}
-	
+
 	var cfg Config
 	if err := json.Unmarshal(data, &cfg); err != nil {
 		return nil, fmt.Errorf("parsing config: %w", err)
 	}
-	
+
 	return &cfg, nil
 }
 
 func (c *Config) Save(beadsDir string) error {
 	configPath := ConfigPath(beadsDir)
-	
+
 	data, err := json.MarshalIndent(c, "", "  ")
 	if err != nil {
 		return fmt.Errorf("marshaling config: %w", err)
 	}
-	
+
 	if err := os.WriteFile(configPath, data, 0600); err != nil {
 		return fmt.Errorf("writing config: %w", err)
 	}
-	
+
 	return nil
 }
 
 func (c *Config) DatabasePath(beadsDir string) string {
-	return filepath.Join(beadsDir, c.Database)
+	backend := c.GetBackend()
+
+	// Treat Database as the on-disk storage location:
+	// - SQLite: filename (default: beads.db)
+	// - Dolt: directory name (default: dolt)
+	//
+	// Backward-compat: early dolt configs wrote "beads.db" even when Backend=dolt.
+	// In that case, treat it as "dolt".
+	if backend == BackendDolt {
+		db := strings.TrimSpace(c.Database)
+		if db == "" || db == "beads.db" {
+			db = "dolt"
+		}
+		if filepath.IsAbs(db) {
+			return db
+		}
+		return filepath.Join(beadsDir, db)
+	}
+
+	// SQLite (default)
+	db := strings.TrimSpace(c.Database)
+	if db == "" {
+		db = "beads.db"
+	}
+	if filepath.IsAbs(db) {
+		return db
+	}
+	return filepath.Join(beadsDir, db)
 }
 
 func (c *Config) JSONLPath(beadsDir string) string {

internal/configfile/configfile_test.go

@@ -8,7 +8,7 @@ import (
 
 func TestDefaultConfig(t *testing.T) {
 	cfg := DefaultConfig()
-	
+
 	if cfg.Database != "beads.db" {
 		t.Errorf("Database = %q, want beads.db", cfg.Database)
 	}
@@ -25,26 +25,26 @@ func TestLoadSaveRoundtrip(t *testing.T) {
 	if err := os.MkdirAll(beadsDir, 0750); err != nil {
 		t.Fatalf("failed to create .beads directory: %v", err)
 	}
-	
+
 	cfg := DefaultConfig()
-	
+
 	if err := cfg.Save(beadsDir); err != nil {
 		t.Fatalf("Save() failed: %v", err)
 	}
-	
+
 	loaded, err := Load(beadsDir)
 	if err != nil {
 		t.Fatalf("Load() failed: %v", err)
 	}
-	
+
 	if loaded == nil {
 		t.Fatal("Load() returned nil config")
 	}
-	
+
 	if loaded.Database != cfg.Database {
 		t.Errorf("Database = %q, want %q", loaded.Database, cfg.Database)
 	}
-	
+
 	if loaded.JSONLExport != cfg.JSONLExport {
 		t.Errorf("JSONLExport = %q, want %q", loaded.JSONLExport, cfg.JSONLExport)
 	}
@@ -52,12 +52,12 @@ func TestLoadSaveRoundtrip(t *testing.T) {
 
 func TestLoadNonexistent(t *testing.T) {
 	tmpDir := t.TempDir()
-	
+
 	cfg, err := Load(tmpDir)
 	if err != nil {
 		t.Fatalf("Load() returned error for nonexistent config: %v", err)
 	}
-	
+
 	if cfg != nil {
 		t.Errorf("Load() = %v, want nil for nonexistent config", cfg)
 	}
@@ -66,22 +66,44 @@ func TestLoadNonexistent(t *testing.T) {
 func TestDatabasePath(t *testing.T) {
 	beadsDir := "/home/user/project/.beads"
 	cfg := &Config{Database: "beads.db"}
-	
+
 	got := cfg.DatabasePath(beadsDir)
 	want := filepath.Join(beadsDir, "beads.db")
-	
+
 	if got != want {
 		t.Errorf("DatabasePath() = %q, want %q", got, want)
 	}
 }
 
+func TestDatabasePath_Dolt(t *testing.T) {
+	beadsDir := "/home/user/project/.beads"
+
+	t.Run("explicit dolt dir", func(t *testing.T) {
+		cfg := &Config{Database: "dolt", Backend: BackendDolt}
+		got := cfg.DatabasePath(beadsDir)
+		want := filepath.Join(beadsDir, "dolt")
+		if got != want {
+			t.Errorf("DatabasePath() = %q, want %q", got, want)
+		}
+	})
+
+	t.Run("backward compat: dolt backend with beads.db field", func(t *testing.T) {
+		cfg := &Config{Database: "beads.db", Backend: BackendDolt}
+		got := cfg.DatabasePath(beadsDir)
+		want := filepath.Join(beadsDir, "dolt")
+		if got != want {
+			t.Errorf("DatabasePath() = %q, want %q", got, want)
+		}
+	})
+}
+
 func TestJSONLPath(t *testing.T) {
 	beadsDir := "/home/user/project/.beads"
-	
+
 	tests := []struct {
-		name       string
-		cfg        *Config
-		want       string
+		name string
+		cfg  *Config
+		want string
 	}{
 		{
 			name: "default",
@@ -99,7 +121,7 @@ func TestJSONLPath(t *testing.T) {
 			want: filepath.Join(beadsDir, "issues.jsonl"),
 		},
 	}
-	
+
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {
 			got := tt.cfg.JSONLPath(beadsDir)
@@ -122,9 +144,9 @@ func TestConfigPath(t *testing.T) {
 
 func TestGetDeletionsRetentionDays(t *testing.T) {
 	tests := []struct {
-		name   string
-		cfg    *Config
-		want   int
+		name string
+		cfg  *Config
+		want int
 	}{
 		{
 			name: "zero uses default",