minor improvements to the execution script

[yymao]

This PR adds some minor improvements to the execution script.

• use the kernel specified in the notebook
• ~allow notebooks to have failed cells~ (reverted, allowing failed cells making it difficult to debug)
• split --no-push option into --no-commit (default behavior is to commit) and --push default behavior is not to push, as most people will not have permission
• use user's own github credential instead of github API
• provide default jupyter path (on NERSC)
• update documentation
• remove unused options (-a, -u, -k, -r)
• fixes #4

This PR also updates the .gitignore file as the original one was for a python-based repo.

[yymao]

This PR is ready for review @drphilmarshall. I've tested it successfully with cron job (See https://github.com/LSSTDESC/DC2-analysis/tree/rendered)