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?

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