Add warning for multiple databases in directory hierarchy (bd-75)

- Implement FindAllDatabases() to scan hierarchy for all .beads directories
- Add DatabaseInfo struct with path, beads dir, and issue count
- Add warnMultipleDatabases() with formatted warning display
- Show active database with ▶ marker and issue counts
- Add comprehensive tests for multi-database detection
- Document warning and solutions in TROUBLESHOOTING.md
- Prevent confusion and database pollution from accidental duplicates

Amp-Thread-ID: https://ampcode.com/threads/T-4941975f-2686-40d0-bc12-aabf38a05890
Co-authored-by: Amp <amp@ampcode.com>

cmd/bd/main.go

@@ -394,6 +394,9 @@ var rootCmd = &cobra.Command{
 		storeActive = true
 		storeMutex.Unlock()
 
+		// Warn if multiple databases detected in directory hierarchy
+		warnMultipleDatabases(dbPath)
+
 		// Check for version mismatch (warn if binary is older than DB)
 		checkVersionMismatch()
 

cmd/bd/worktree.go

@@ -6,6 +6,8 @@ import (
 	"os/exec"
 	"path/filepath"
 	"strings"
+
+	"github.com/steveyegge/beads"
 )
 
 // isGitWorktree detects if the current directory is in a git worktree
@@ -91,3 +93,55 @@ func truncateForBox(path string, maxLen int) string {
 	// Truncate with ellipsis
 	return "..." + path[len(path)-(maxLen-3):]
 }
+
+// warnMultipleDatabases prints a warning if multiple .beads databases exist
+// in the directory hierarchy, to prevent confusion and database pollution
+func warnMultipleDatabases(currentDB string) {
+	databases := beads.FindAllDatabases()
+	if len(databases) <= 1 {
+		return // Only one database found, no warning needed
+	}
+
+	// Find which database is active
+	activeIdx := -1
+	for i, db := range databases {
+		if db.Path == currentDB {
+			activeIdx = i
+			break
+		}
+	}
+
+	fmt.Fprintln(os.Stderr)
+	fmt.Fprintln(os.Stderr, "╔══════════════════════════════════════════════════════════════════════════╗")
+	fmt.Fprintf(os.Stderr, "║ WARNING: %d beads databases detected in directory hierarchy             ║\n", len(databases))
+	fmt.Fprintln(os.Stderr, "╠══════════════════════════════════════════════════════════════════════════╣")
+	fmt.Fprintln(os.Stderr, "║ Multiple databases can cause confusion and database pollution.          ║")
+	fmt.Fprintln(os.Stderr, "║                                                                          ║")
+	
+	for i, db := range databases {
+		isActive := (i == activeIdx)
+		issueInfo := ""
+		if db.IssueCount >= 0 {
+			issueInfo = fmt.Sprintf(" (%d issues)", db.IssueCount)
+		}
+		
+		marker := " "
+		if isActive {
+			marker = "▶"
+		}
+		
+		line := fmt.Sprintf("%s %s%s", marker, db.BeadsDir, issueInfo)
+		fmt.Fprintf(os.Stderr, "║ %-72s ║\n", truncateForBox(line, 72))
+	}
+	
+	fmt.Fprintln(os.Stderr, "║                                                                          ║")
+	if activeIdx == 0 {
+		fmt.Fprintln(os.Stderr, "║ Currently using the closest database (▶). This is usually correct.      ║")
+	} else {
+		fmt.Fprintln(os.Stderr, "║ WARNING: Not using the closest database! Check your BEADS_DB setting.   ║")
+	}
+	fmt.Fprintln(os.Stderr, "║                                                                          ║")
+	fmt.Fprintln(os.Stderr, "║ RECOMMENDED: Consolidate or remove unused databases to avoid confusion. ║")
+	fmt.Fprintln(os.Stderr, "╚══════════════════════════════════════════════════════════════════════════╝")
+	fmt.Fprintln(os.Stderr)
+}