Remove nodb_prefix.txt in favor of config.yaml

Remove support for the legacy .beads/nodb_prefix.txt file and use
the cleaner config.yaml approach exclusively for setting the issue
prefix. This simplifies the configuration system and makes it more
consistent.

Changes:
- Remove nodb_prefix.txt creation in cmd/bd/init.go
- Remove nodb_prefix.txt check in cmd/bd/nodb.go detectPrefix()
- Update error message to recommend config.yaml instead
- Update documentation to reflect config.yaml-only approach

New prefix detection order for --no-db mode:
1. issue-prefix in config.yaml (if set)
2. Common prefix from existing issues (if all share same prefix)
3. Current directory name (fallback)

Users should now set the prefix in .beads/config.yaml:
  issue-prefix: "myproject"

Generated with [Claude Code](https://claude.ai/code)
via [Happy](https://happy.engineering)

Co-Authored-By: Claude <noreply@anthropic.com>
Co-Authored-By: Happy <yesreply@happy.engineering>

cmd/bd/init.go

@@ -20,7 +20,7 @@ var initCmd = &cobra.Command{
 	Long: `Initialize bd in the current directory by creating a .beads/ directory
 and database file. Optionally specify a custom issue prefix.
 
-With --no-db: creates .beads/ directory and nodb_prefix.txt file instead of SQLite database.`,
+With --no-db: creates .beads/ directory and issues.jsonl file instead of SQLite database.`,
 	Run: func(cmd *cobra.Command, _ []string) {
 		prefix, _ := cmd.Flags().GetString("prefix")
 		quiet, _ := cmd.Flags().GetBool("quiet")
@@ -96,14 +96,8 @@ With --no-db: creates .beads/ directory and nodb_prefix.txt file instead of SQLi
 			os.Exit(1)
 		}
 
-		// Handle --no-db mode: create nodb_prefix.txt instead of database
+		// Handle --no-db mode: create issues.jsonl file instead of database
 		if noDb {
-			prefixFile := filepath.Join(localBeadsDir, "nodb_prefix.txt")
-			if err := os.WriteFile(prefixFile, []byte(prefix+"\n"), 0644); err != nil {
-				fmt.Fprintf(os.Stderr, "Error: failed to write prefix file: %v\n", err)
-				os.Exit(1)
-			}
-
 			// Create empty issues.jsonl file
 			jsonlPath := filepath.Join(localBeadsDir, "issues.jsonl")
 			if _, err := os.Stat(jsonlPath); os.IsNotExist(err) {