Mmf-setup

- Resolves issue 15.
- Use `$BASH_SOURCE{0}` to get `BIN_DIR` (resolves issue 16)
- Added `nbinit(hgroot)` option to add `hg root` to `sys.path` (issue 13)

- Changed option to `--clean-all` (resolves issue 7)
- Updated the notebook style (added `\Tr`, fixed output overflow issue)
- Added pip option mmf_setup[nbextensions]
- Removed `'EnableNBExtensionApp'` dependence which broke new Jupyter (resolves issue
12)
- Added some files for initializing setup on Sage Mathcloud (SMC) (resolves issue 14).
- Added `mmf_initial_setup` script and some init files (`.inputrc`, `.hgrc`,
`.bash_aliases`).
- Run with `mmf_setup smc`
- Removed old extension manager since nbextensions are quite good now.

- Added cupdate command (resolves issue 4)
- Fixed bug with ccommit where it did not accept a list of files
(issue 6)
- Issue commands in a context to provide a robust mechanism for
recovery (issue 5)