I don't think its as simple as first thoughts indicate, project files don't get stored in the tree by default..
What is the purpose of `base_path` project setting? It's logical to use it in conjunction with project's source tree. Such that any relative paths referenced in `[files]` would be considered relative to the `base_path`. Of course, other files may be from outer trees, but those could stay absolute.
Btw, why there are `%2F` used instead of actual `/` in file path in `[files]` section?