I think this line:

should rather be this:

collectSpecificDependencies(result, baseGrammar, baseGrammar, includedName, baseGrammar.repository);

Also, this line:

should be this:

collectSpecificDependencies(result, baseGrammar, selfGrammar, includedName, selfGrammar.repository);

Let's say source.md embeds source.css and a rule in source.css references source.md#link.
Then with the logic in main, a rule in source.css referencing source.md#link would look up link in its local repository (first repositories of this rule or parent rules, then the repository of source.css), but not in the repository of source.md.