Move files from root to appropriate folders

Fixes https://github.com/numenta/nupic/issues/972 (original ticket)
which was subdivided into 4 parts:
https://github.com/numenta/nupic/issues/1004 (`conf` folder)
https://github.com/numenta/nupic/issues/978 (`githooks` folder)
https://github.com/numenta/nupic/issues/1012 (`docker` folder)
https://github.com/numenta/nupic/issues/977 (`doxyfile` file)