fix(dbml): resolve commented cross-file // Ref: lines

Commented refs are collected per file and resolved against the combined
model after all inputs are loaded (directory, --from-list, merge, jobs).
Matched refs become FKs and relationships; duplicates of existing FKs are
skipped; missing targets are skipped with a warning; column type
mismatches warn.

Also keep reused index names within a DBML table instead of overwriting,
give a second FK to the same table a distinct relationship name, and make
the pgsql writer match relationships to FKs by name first.

cmd/relspec/convert.go

@@ -229,6 +229,7 @@ func runConvert(cmd *cobra.Command, args []string) error {
 	if err != nil {
 		return fmt.Errorf("failed to read source: %w", err)
 	}
+	finalizeCommentedRefs(db, stderrWarn)
 
 	fmt.Fprintf(os.Stderr, "      ✓ Successfully read database '%s'\n", db.Name)
 	fmt.Fprintf(os.Stderr, "      Found: %d schema(s)\n", len(db.Schemas))
@@ -261,6 +262,18 @@ func runConvert(cmd *cobra.Command, args []string) error {
 	return nil
 }
 
+// finalizeCommentedRefs resolves DBML `// Ref:` comments against the fully
+// loaded model and warns about refs whose target is not loaded.
+func finalizeCommentedRefs(db *models.Database, warn func(string)) {
+	for _, w := range dbml.ResolveCommentedRefs(db, true) {
+		warn(w)
+	}
+}
+
+func stderrWarn(msg string) {
+	fmt.Fprintf(os.Stderr, "      ⚠ %s\n", msg)
+}
+
 func readDatabaseListForConvert(dbType string, files []string) (*models.Database, error) {
 	if len(files) == 0 {
 		return nil, fmt.Errorf("file list is empty")

cmd/relspec/job.go

@@ -578,6 +578,7 @@ func runMergeJob(rj *resolvedJob, lg *jobLogger) error {
 		lg.logf("merging: %s", inputLabel(ri))
 		merge.MergeDatabases(base, db, opts)
 	}
+	finalizeCommentedRefs(base, func(w string) { lg.logf("warning: %s", w) })
 	base.UpdateDate()
 	return writeJobOutput(rj, base, lg)
 }
@@ -814,6 +815,7 @@ func readJobInputs(rj *resolvedJob, lg *jobLogger) (*models.Database, error) {
 	if base == nil {
 		return nil, fmt.Errorf("no inputs produced a database")
 	}
+	finalizeCommentedRefs(base, func(w string) { lg.logf("warning: %s", w) })
 	return base, nil
 }
 

cmd/relspec/merge.go

@@ -248,6 +248,7 @@ func runMerge(cmd *cobra.Command, args []string) error {
 	}
 
 	result := merge.MergeDatabases(targetDB, sourceDB, opts)
+	finalizeCommentedRefs(targetDB, stderrWarn)
 
 	// Update timestamp
 	targetDB.UpdateDate()

cmd/relspec/templ.go

@@ -114,6 +114,7 @@ func runTempl(cmd *cobra.Command, args []string) error {
 	if err != nil {
 		return fmt.Errorf("failed to read source: %w", err)
 	}
+	finalizeCommentedRefs(db, stderrWarn)
 
 	// Print database stats
 	schemaCount := len(db.Schemas)