IE Mako + JS Refactor

This is a massive refactor of the JS + templates to try and separate out code that is general to all IEs from code that is specific to IPython as a Galaxy IE. 

## Templates

A notebook is now `{name}.mako` in the `templates/` directory. It loads `ie.mako` which contains numerous routines for handling various IE aspects. Much of the conf file preparation was also moved into `ie.mako` as we should probably standardise the `conf.yaml` file across all IEs. Only the IPyNB specific code remains in `ipython.mako`. 

## JS

JS was refactored into two files, one containing IE generic JS, and one containing IPython specific JS (the login routines). There is room for improvement there, but I'm not that much of a JS person so help is welcome.

## Final Notes

With this progress done, we can probably split out a "IE base" repository containing just what's needed to bootstrap an IE.
sys, time, shutil and tempfile are not used here.