fix: allow yaml-only config operations without database (GH#536)

Users could not run 'bd config set no-db true' without already having a
database, creating a chicken-and-egg problem. The PersistentPreRunE
would fail with 'no beads database found' before the config command
could even run.

The fix detects when a yaml-only config operation is being attempted
(config set/get with keys like no-db, no-daemon, sync.branch, etc.)
and allows it to proceed without requiring a database.

Before:
  $ bd config set no-db true
  Error: no beads database found

After:
  $ bd config set no-db true
  Set no-db = true (in config.yaml)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/config_test.go

@@ -6,6 +6,7 @@ import (
 	"path/filepath"
 	"testing"
 
+	"github.com/steveyegge/beads/internal/config"
 	"github.com/steveyegge/beads/internal/storage/sqlite"
 )
 
@@ -148,6 +149,52 @@ func TestConfigNamespaces(t *testing.T) {
 	}
 }
 
+// TestYamlOnlyConfigWithoutDatabase verifies that yaml-only config keys
+// (like no-db, no-daemon) can be set/get without requiring a SQLite database.
+// This is the fix for GH#536 - the chicken-and-egg problem where you couldn't
+// run `bd config set no-db true` without first having a database.
+func TestYamlOnlyConfigWithoutDatabase(t *testing.T) {
+	// Create a temp directory with only config.yaml (no database)
+	tmpDir, err := os.MkdirTemp("", "bd-test-yaml-config-*")
+	if err != nil {
+		t.Fatalf("Failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	if err := os.MkdirAll(beadsDir, 0755); err != nil {
+		t.Fatalf("Failed to create .beads dir: %v", err)
+	}
+
+	// Create config.yaml with a prefix but NO database
+	configPath := filepath.Join(beadsDir, "config.yaml")
+	if err := os.WriteFile(configPath, []byte("prefix: test\n"), 0644); err != nil {
+		t.Fatalf("Failed to create config.yaml: %v", err)
+	}
+
+	// Create empty issues.jsonl (simulates fresh clone)
+	jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
+	if err := os.WriteFile(jsonlPath, []byte(""), 0644); err != nil {
+		t.Fatalf("Failed to create issues.jsonl: %v", err)
+	}
+
+	// Test that IsYamlOnlyKey correctly identifies yaml-only keys
+	yamlOnlyKeys := []string{"no-db", "no-daemon", "no-auto-flush", "json", "sync.branch", "routing.mode"}
+	for _, key := range yamlOnlyKeys {
+		if !config.IsYamlOnlyKey(key) {
+			t.Errorf("Expected %q to be a yaml-only key", key)
+		}
+	}
+
+	// Test that non-yaml-only keys are correctly identified
+	nonYamlKeys := []string{"jira.url", "linear.team_id", "status.custom"}
+	for _, key := range nonYamlKeys {
+		if config.IsYamlOnlyKey(key) {
+			t.Errorf("Expected %q to NOT be a yaml-only key", key)
+		}
+	}
+}
+
 // setupTestDB creates a temporary test database
 func setupTestDB(t *testing.T) (*sqlite.SQLiteStorage, func()) {
 	tmpDir, err := os.MkdirTemp("", "bd-test-config-*")

cmd/bd/main.go

@@ -434,7 +434,14 @@ var rootCmd = &cobra.Command{
 				// Allow some commands to run without a database
 				// - import: auto-initializes database if missing
 				// - setup: creates editor integration files (no DB needed)
-				if cmd.Name() != "import" && cmd.Name() != "setup" {
+				// - config set/get for yaml-only keys: writes to config.yaml, not SQLite (GH#536)
+				isYamlOnlyConfigOp := false
+				if (cmd.Name() == "set" || cmd.Name() == "get") && cmd.Parent() != nil && cmd.Parent().Name() == "config" {
+					if len(args) > 0 && config.IsYamlOnlyKey(args[0]) {
+						isYamlOnlyConfigOp = true
+					}
+				}
+				if cmd.Name() != "import" && cmd.Name() != "setup" && !isYamlOnlyConfigOp {
 					// No database found - provide context-aware error message
 					fmt.Fprintf(os.Stderr, "Error: no beads database found\n")