Merge pull request #751 from DavidRagazzi/master

Integration with nupic.core API
Change README to simplify environment variable documentation.
Update README with Marek's comments and update Dockerfile accordingly.
Restore run_tests.sh
Merge pull request #783 from scottpurdy/readme

Change README to simplify environment variable documentation.
Fixup run_tests.sh to do a cleaner pushd/popd directory change, update typo in help text
fix env.sh reference (removed)
add make clean target
mention make clean in Readme
do not clean temp build files be default

should speed up re-build process as only changed .o files are compiled again.
Use make clean to start fresh --eg when strange errors occur.
Merge pull request #785 from oxtopus/restore-run_tests.sh

Restore run_tests.sh
prepare folders each time
fix make distclean target
update SHA

36b767834dc9a18dcb6f8cd807e6d01e
Merge pull request #788 from breznak/custom_targets

keep compiled files between compiles, make distclean
Merge pull request #10 from numenta/master

Rebase fork