In Windows, under AppData/Roaming/MoI, I have the folders:
/commands (for add on commands, with underline preface. (e.g. _angle))
/customui
/objects
/snapshots
/startup

also files :
MiniSidepane.js, and two MOD versions (unused).
moi.ini
moi_v2_license.key
moi_v3_license.key

Stock MoI commands remain in C:\ProgramFiles\Moi4.0 beta(date) folder.
- Brian