Remove git submodule in favor of CMake commands

Fixes #798.
Fixes #634.

Removed nta git submodule, replaced with CMake commands to manually clone, fetch, and checkout nupic.core repository.  This also allows overriding the defaults on the command line via NUPIC_CORE_REMOTE, for the remote repository url, and NUPIC_CORE_COMMITISH, for the specific sha.

There are several advantages to this approach:

1. No git submodules (nupic git repository is no longer explicitly coupled to git://github.com/numenta/nupic.core.git)
2. ~~CMakeLists.txt~~ `.nupic_modules` is the ground truth for nupic.core version dependency
3. User can override NUPIC_CORE_REMOTE and NUPIC_CORE_COMMITISH at-will, if they are not using the official nupic.core repository.
4. Developer can make changes in nta/ and push to remote repository of their choosing