Cache: merged get_deps and query_file

- Still need to clean everything up and verify it works
tests: Cache test now tests getting deps
app: shorten method name to get deps from Cache
Cache: more cleanup post method-merge

- Fixed virtual libs being added to cache as filenames instead of
  objects
- Fixed usage of App::SharedLibraryDeps::BinFile and
  App::SharedLibraryDeps::LibFile everywhere