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.

pkg/merge/merge.go

@@ -91,6 +91,45 @@ func (r *MergeResult) merge(target, source *models.Database, opts *MergeOptions)
 	if !opts.SkipDomains {
 		r.mergeDomains(target, source)
 	}
+
+	mergeDatabaseMetadata(target, source)
+}
+
+// mergeDatabaseMetadata adds missing metadata keys and unions []string values,
+// so per-file reader state (e.g. pending DBML commented refs) survives a merge.
+func mergeDatabaseMetadata(target, source *models.Database) {
+	if len(source.Metadata) == 0 {
+		return
+	}
+	if target.Metadata == nil {
+		target.Metadata = make(map[string]any, len(source.Metadata))
+	}
+	for key, srcVal := range source.Metadata {
+		tgtVal, exists := target.Metadata[key]
+		if !exists {
+			if list, ok := srcVal.([]string); ok {
+				srcVal = append([]string(nil), list...)
+			}
+			target.Metadata[key] = srcVal
+			continue
+		}
+		tgtList, tgtOK := tgtVal.([]string)
+		srcList, srcOK := srcVal.([]string)
+		if !tgtOK || !srcOK {
+			continue
+		}
+		seen := make(map[string]bool, len(tgtList))
+		for _, v := range tgtList {
+			seen[v] = true
+		}
+		for _, v := range srcList {
+			if !seen[v] {
+				tgtList = append(tgtList, v)
+				seen[v] = true
+			}
+		}
+		target.Metadata[key] = tgtList
+	}
 }
 
 func (r *MergeResult) mergeSchemaContents(target, source *models.Schema, opts *MergeOptions) {

pkg/merge/merge_test.go

@@ -721,3 +721,32 @@ func TestComplexMerge(t *testing.T) {
 		t.Error("Expected ukey_users_guid constraint to exist")
 	}
 }
+
+func TestMergeDatabases_Metadata(t *testing.T) {
+	target := &models.Database{Metadata: map[string]any{
+		"refs": []string{"a", "b"},
+		"name": "target",
+	}}
+	source := &models.Database{Metadata: map[string]any{
+		"refs":  []string{"b", "c"},
+		"name":  "source",
+		"extra": []string{"x"},
+	}}
+
+	MergeDatabases(target, source, nil)
+
+	if got := target.Metadata["refs"].([]string); strings.Join(got, ",") != "a,b,c" {
+		t.Errorf("refs = %v, want [a b c]", got)
+	}
+	if got := target.Metadata["name"]; got != "target" {
+		t.Errorf("name = %v, want target (existing scalar keys are kept)", got)
+	}
+	extra := target.Metadata["extra"].([]string)
+	if strings.Join(extra, ",") != "x" {
+		t.Errorf("extra = %v, want [x]", extra)
+	}
+	source.Metadata["extra"].([]string)[0] = "changed"
+	if extra[0] != "x" {
+		t.Error("copied slice must not alias the source")
+	}
+}