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I think this discussion is getting off track.

It is certainly reasonable (or at least I hope it is) to write
TUI/
  Main.py
and expect unix users to execute Main.py, for example:
alias tui <tui_root>/TUI/Main.py

The problem comes when bundlebuilder helpfully pulls Main.py out of TUI and puts up up at the main level. It seems an odd arrangement of files to me -- I'd much rather stuff all my app's files into a directory and make that a package (to reduce the danger of namespace collisions).

I really don't see the importing issue coming up here. I was hoping bundlebuilder would simply execute the file TUI/Main.py without moving it. It doesn't need to import anything, it just needs to execute the file.

Anyway, I do agree it's not that hard to work around. It just seems a shame that bundlebuilder moves files around without being asked. Once one realizes what is going on, one can figure out workarounds -- such as making the main file movable or writing a stupid 2-line extra script to call the main file.