Hello Lorenzo, I think that the problem you described is unrelated to the filename system. It already exists in the "legacy" libraries. It is why the order of the libraries is sometimes important (if two libraries contain a module with the same name, CvPcb and pcbnew pick the one from the topmost library).
This is easily fixable (by storing both the library name and the module name in board file), and to the best of my knowledge, it is being worked on. Regards, Thiadmer Riemersma
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