Architect should be the only thing messing with these files (or perhaps source control). store.local, store.direct is never going to produce good results.
To fix this you should move all stores and models back to stores/ models/ directory. Also the local copies I can see you've created yourself. I would remove those and duplicate the "direct" ones and then name them ContactLocal, PeopleLocal and add in your data using Architect.
Sencha Architect Development Team