There are some valid use cases for allowing these files to be outside
the project directory. Relax the restriction, and include a strong
warning in the documentation.
Before this refactoring, presets had a simple flag that marked them
as "user" or "not user", and checking the file graph of two files
was as simple as checking this flag. This only allowed for two files
in the graph. Generalize the code to allow for arbitrarily many files
in the graph.
