"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
Updated link in CONTRIBUTING.md
Merge pull request #750 from rhyolight/update-readme

Updated link in CONTRIBUTING.md
A improved version of CMake file

-Removed standard libraries (libapr, libs,etc) stuff;
Fixed -lc++abi issue
Fixed -gfull issue
Adding readme file
Adding content to spatial pooler example readme
Merge pull request #754 from zacg/master

Readme for Spatial Pooler Example
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.
"ie" replaced by "i.e."
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.