fix(init,import): preserve metadata.json and improve prefix detection

- bd init now preserves existing metadata.json settings instead of
  overwriting with defaults (bd-zai)
- bd init detects existing JSONL filename (beads.jsonl vs issues.jsonl)
  when creating new metadata.json
- bd import now correctly reports prefix source ("issues" vs "directory")
- bd import avoids using ".beads" as prefix when run from inside .beads/

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

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

cmd/bd/import.go

@@ -200,20 +200,29 @@ NOTE: Import requires direct database access and does not work with daemon mode.
 		}
 
 		// Check if database needs initialization (prefix not set)
-		// Detect prefix from the imported issues
+		// Detect prefix from the imported issues (bd-8an fix)
 		initCtx := rootCtx
 		configuredPrefix, err2 := store.GetConfig(initCtx, "issue_prefix")
 		if err2 != nil || strings.TrimSpace(configuredPrefix) == "" {
 			// Database exists but not initialized - detect prefix from issues
 			detectedPrefix := detectPrefixFromIssues(allIssues)
+			prefixSource := "issues"
 			if detectedPrefix == "" {
 				// No issues to import or couldn't detect prefix, use directory name
+				// But avoid using ".beads" as prefix - go up one level
 				cwd, err := os.Getwd()
 				if err != nil {
 					fmt.Fprintf(os.Stderr, "Error: failed to get current directory: %v\n", err)
 					os.Exit(1)
 				}
-				detectedPrefix = filepath.Base(cwd)
+				dirName := filepath.Base(cwd)
+				if dirName == ".beads" || dirName == "beads" {
+					// Running from inside .beads/ - use parent directory
+					detectedPrefix = filepath.Base(filepath.Dir(cwd))
+				} else {
+					detectedPrefix = dirName
+				}
+				prefixSource = "directory"
 			}
 			detectedPrefix = strings.TrimRight(detectedPrefix, "-")
 
@@ -222,7 +231,7 @@ NOTE: Import requires direct database access and does not work with daemon mode.
 				os.Exit(1)
 			}
 
-			fmt.Fprintf(os.Stderr, "✓ Initialized database with prefix '%s' (detected from issues)\n", detectedPrefix)
+			fmt.Fprintf(os.Stderr, "✓ Initialized database with prefix '%s' (detected from %s)\n", detectedPrefix, prefixSource)
 		}
 
 		// Phase 2: Use shared import logic

cmd/bd/init.go

@@ -294,9 +294,30 @@ With --stealth: configures global git settings for invisible beads usage:
 			}
 		}
 
-		// Create metadata.json for database metadata
+		// Create or preserve metadata.json for database metadata (bd-zai fix)
 		if useLocalBeads {
-			cfg := configfile.DefaultConfig()
+			// First, check if metadata.json already exists
+			existingCfg, err := configfile.Load(localBeadsDir)
+			if err != nil {
+				fmt.Fprintf(os.Stderr, "Warning: failed to load existing metadata.json: %v\n", err)
+			}
+
+			var cfg *configfile.Config
+			if existingCfg != nil {
+				// Preserve existing config
+				cfg = existingCfg
+			} else {
+				// Create new config, detecting JSONL filename from existing files
+				cfg = configfile.DefaultConfig()
+				// Check if beads.jsonl exists but issues.jsonl doesn't (legacy)
+				issuesPath := filepath.Join(localBeadsDir, "issues.jsonl")
+				beadsPath := filepath.Join(localBeadsDir, "beads.jsonl")
+				if _, err := os.Stat(beadsPath); err == nil {
+					if _, err := os.Stat(issuesPath); os.IsNotExist(err) {
+						cfg.JSONLExport = "beads.jsonl" // Legacy filename
+					}
+				}
+			}
 			if err := cfg.Save(localBeadsDir); err != nil {
 				fmt.Fprintf(os.Stderr, "Warning: failed to create metadata.json: %v\n", err)
 				// Non-fatal - continue anyway