Save As Project does not include all javascript dependencies

I've noticed that when saving as a project, not all javascript files end up in the project's /code directory.

For example, if a patcher has [js myfile.js], and myfile.js requires dependency.js, then only myfile.js is copied into /code. The other file, dependency.js, appears in the list of files in the project window, but has to be manually copied to the local directory.

Is this intentional? And is there a way to make sure that all dependencies are included? Manually adding each file in the project window is not a great way to work.

(I have tried selecting "Always Localise ..." then reloading, but no luck).