stop relying on `.gitmodules` to determine submodule existence

[jhedwardyang]

$ rm -rf one 
$ git commit -m "Deleting one" one
$ git meta push origin HEAD:demo
Error: the path 'one' does not exist in the given tree                                                                                                                                                                                    
    at Error (native)

[jhedwardyang]

Relates to #277. Probably fixable together.

[bpeabody]

I need to overhaul the system to derive submodule existence from the tree -- a submodule exists at path X iff there is a COMMIT type entry at X.