refactor: remove unused bd pin/unpin/hook commands (bd-x0zl)

Analysis found these commands are dead code:
- gt never calls `bd pin` - uses `bd update --status=pinned` instead
- Beads.Pin() wrapper exists but is never called
- bd hook functionality duplicated by gt mol status
- Code comment says "pinned field is cosmetic for bd hook visibility"

Removed:
- cmd/bd/pin.go
- cmd/bd/unpin.go
- cmd/bd/hook.go

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

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

cmd/bd/doctor/config_values.go

@@ -316,6 +316,10 @@ func checkMetadataConfigValues(repoPath string) []string {
 
 	// Validate jsonl_export filename
 	if cfg.JSONLExport != "" {
+		switch cfg.JSONLExport {
+		case "deletions.jsonl", "interactions.jsonl", "molecules.jsonl":
+			issues = append(issues, fmt.Sprintf("metadata.json jsonl_export: %q is a system file and should not be configured as a JSONL export (expected issues.jsonl)", cfg.JSONLExport))
+		}
 		if strings.Contains(cfg.JSONLExport, string(os.PathSeparator)) || strings.Contains(cfg.JSONLExport, "/") {
 			issues = append(issues, fmt.Sprintf("metadata.json jsonl_export: %q should be a filename, not a path", cfg.JSONLExport))
 		}
@@ -353,7 +357,7 @@ func checkDatabaseConfigValues(repoPath string) []string {
 	}
 
 	// Open database in read-only mode
-	db, err := sql.Open("sqlite3", "file:"+dbPath+"?mode=ro")
+	db, err := sql.Open("sqlite3", sqliteConnString(dbPath, true))
 	if err != nil {
 		return issues // Can't open database, skip
 	}