So I can't interact with my classes because my package isn't a directory ?
Hmmm, I would expect it to return true on the isDirectory().
Can you debug it a bit further, so that we see which VFS's FileSystem instance / impl is used.
e.g. step into VirtualFile::isDirectory and see which mount.getFileSystem() gets used
At which point you are using your code?
If the VFS didn't yet properly mount the zip/jar files, then this might be the root of the problem.
e.g. zip/jar files need to be explicitly mounted in order for VFS to understand zip/jar structure