The file extensions you're using are conflicting with established formats. MOD (for modules) is a common extension of ProTracker mod music format and MST is save format of Mesen emulator. Since NM is a windows application and Windows (along with all modern operating systems) support extensions that are longer than 3 characters, how about more descriptive (and conflict-free) extensions as follows:
.nesmodule - for modules
.nesproject - for project files.
.nesmodule - for modules
.nesproject - for project files.