fix: write startup config keys to config.yaml instead of SQLite (GH#536)

`bd config set no-db true` now correctly writes to config.yaml instead of
SQLite. Previously, startup flags like no-db, no-daemon, no-auto-flush were
stored in SQLite but read from config.yaml at startup - making the command
appear to work while having no effect.

This adds:
- yaml_config.go: Defines yaml-only keys and provides SetYamlConfig/GetYamlConfig
- Updated config set/get commands to route yaml-only keys appropriately
- Comprehensive tests for yaml config handling

Startup flags affected: no-db, no-daemon, no-auto-flush, no-auto-import,
json, auto-start-daemon, flush-debounce, lock-timeout, git.*, sync.*, routing.*

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

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

cmd/bd/config.go

@@ -7,6 +7,7 @@ import (
 	"strings"
 
 	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/config"
 	"github.com/steveyegge/beads/internal/syncbranch"
 )
 
@@ -49,17 +50,38 @@ var configSetCmd = &cobra.Command{
 	Short: "Set a configuration value",
 	Args:  cobra.ExactArgs(2),
 	Run: func(_ *cobra.Command, args []string) {
-		// Config operations work in direct mode only
+		key := args[0]
+		value := args[1]
+
+		// Check if this is a yaml-only key (startup settings like no-db, no-daemon, etc.)
+		// These must be written to config.yaml, not SQLite, because they're read
+		// before the database is opened. (GH#536)
+		if config.IsYamlOnlyKey(key) {
+			if err := config.SetYamlConfig(key, value); err != nil {
+				fmt.Fprintf(os.Stderr, "Error setting config: %v\n", err)
+				os.Exit(1)
+			}
+
+			if jsonOutput {
+				outputJSON(map[string]interface{}{
+					"key":      key,
+					"value":    value,
+					"location": "config.yaml",
+				})
+			} else {
+				fmt.Printf("Set %s = %s (in config.yaml)\n", key, value)
+			}
+			return
+		}
+
+		// Database-stored config requires direct mode
 		if err := ensureDirectMode("config set requires direct database access"); err != nil {
 			fmt.Fprintf(os.Stderr, "Error: %v\n", err)
 			os.Exit(1)
 		}
 
-		key := args[0]
-		value := args[1]
-
 		ctx := rootCtx
-		
+
 		// Special handling for sync.branch to apply validation
 		if strings.TrimSpace(key) == syncbranch.ConfigKey {
 			if err := syncbranch.Set(ctx, store, value); err != nil {
@@ -89,25 +111,46 @@ var configGetCmd = &cobra.Command{
 	Short: "Get a configuration value",
 	Args:  cobra.ExactArgs(1),
 	Run: func(cmd *cobra.Command, args []string) {
-		// Config operations work in direct mode only
+		key := args[0]
+
+		// Check if this is a yaml-only key (startup settings)
+		// These are read from config.yaml via viper, not SQLite. (GH#536)
+		if config.IsYamlOnlyKey(key) {
+			value := config.GetYamlConfig(key)
+
+			if jsonOutput {
+				outputJSON(map[string]interface{}{
+					"key":      key,
+					"value":    value,
+					"location": "config.yaml",
+				})
+			} else {
+				if value == "" {
+					fmt.Printf("%s (not set in config.yaml)\n", key)
+				} else {
+					fmt.Printf("%s\n", value)
+				}
+			}
+			return
+		}
+
+		// Database-stored config requires direct mode
 		if err := ensureDirectMode("config get requires direct database access"); err != nil {
 			fmt.Fprintf(os.Stderr, "Error: %v\n", err)
 			os.Exit(1)
 		}
 
-		key := args[0]
-
 		ctx := rootCtx
 		var value string
 		var err error
-		
+
 		// Special handling for sync.branch to support env var override
 		if strings.TrimSpace(key) == syncbranch.ConfigKey {
 			value, err = syncbranch.Get(ctx, store)
 		} else {
 			value, err = store.GetConfig(ctx, key)
 		}
-		
+
 		if err != nil {
 			fmt.Fprintf(os.Stderr, "Error getting config: %v\n", err)
 			os.Exit(1)