`CustomFile` in `mem_fs` can only be read once

More context: #5374

Running mounted commands was broken because `CustomFile` is backed by a `VirtualFile`, and `VirtualFile` stores its offset whereas other file types are just pointers to file data. The issue was worked around in #5374, but more uses of `copy_reference` (which creates `CustomFile`s) exist and I'm not sure what other code paths are broken as a result.