Apply module scope to file validation checks

internal/validation/markdown_check.go

@@ -17,7 +17,7 @@ func checkMarkdownLinks(ctx context.Context, tree *CandidateTree, enforceCheckou
 	}
 	cache := newMarkdownCache(tree)
 	var findings []Finding
-	for _, entry := range tree.Entries() {
+	for _, entry := range tree.inputEntries {
 		if err := ctx.Err(); err != nil {
 			return &Failure{Check: MarkdownLinks, Findings: findings, Cause: err}
 		}