Add bd migrate command for database upgrades (bd-164)

- Implement bd migrate command with detection, version checking, and cleanup
- Update daemon to suggest bd migrate for version mismatches
- Enhance CLI version warnings to recommend bd migrate
- Add comprehensive tests for migration scenarios
- Document migration workflow in QUICKSTART.md and AGENTS.md

Completes bd-164 and epic bd-159

Amp-Thread-ID: https://ampcode.com/threads/T-34ea4682-8c48-44c2-8421-dc40f867773b
Co-authored-by: Amp <amp@ampcode.com>

cmd/bd/main.go

@@ -1032,7 +1032,8 @@ func checkVersionMismatch() {
 		} else if cmp > 0 {
 			// Binary is newer than database
 			fmt.Fprintf(os.Stderr, "%s\n", yellow("⚠️  Your binary appears NEWER than the database."))
-			fmt.Fprintf(os.Stderr, "%s\n\n", yellow("⚠️  The database will be upgraded automatically."))
+			fmt.Fprintf(os.Stderr, "%s\n", yellow("⚠️  Run 'bd migrate' to check for and migrate old database files."))
+			fmt.Fprintf(os.Stderr, "%s\n\n", yellow("⚠️  The current database version will be updated automatically."))
 			// Update stored version to current
 			_ = store.SetMetadata(ctx, "bd_version", Version)
 		}