"htmtest" only with PyNode tests moved to "/tests"

"htmtest" was splitted in two versions: one only with C++ tests which
was moved to "nupic.core" and another only with PyNode (c++ region
implementation for Python projects).
.gitignored updated to ignore "/nta" folder
CMake file is able to build submodules
A improved version of CMake file

-Removed standard libraries (libapr, libs,etc) stuff;
Fixed -lc++abi issue
Fixed -gfull issue
Update .gitmodules
Update .gitmodules
Updated SHA
Update SHA
Refactoring: extracting methods and params.

Preparing for higher granularity singature of the functionality in the
runPermutations function by extracting many functions and breaking out
parameters.
Extracted CLI from Permutations Runner.

- Pulled all options parsing into run_swarm.py.
- Refactored runPermutations into lots of little pieces.
- Replaced runPermutations with three functions:
  - runWithConfig (accepts config dict)
  - runWithJsonFile (accepts path to JSON config file)
  - runWithPermutationsScript (accepts path to permutations.py)
- Updated run_swarms to call into permutations_runner.runWithJsonFile or
  .runWithPermutationsScript

So CLI is still entact, and new public functions exist for using the
permutations_runner directly:

- nupic.swarming.permutations_runner.runWithConfig
- nupic.swarming.permutations_runner.runWithJsonFile
- nupic.swarming.permutations_runner.runWithPermutationsScript
Removed unused imports.
Cleanup and documentation.

Doxygen docs, code cleanup.
Replaced "nupic.core" to "nupic_core" (compliance with file name convention)
Update SHA
Force Travis to compile
"htmtest" only with PyNode tests moved to "/tests"

"htmtest" was splitted in two versions: one only with C++ tests which
was moved to "nupic.core" and another only with PyNode (c++ region
implementation for Python projects).
.gitignored updated to ignore "/nta" folder
CMake file is able to build submodules