Vim: indent with tabs, not spaces. Clean up .vimrc

The only real change this makes is to set the option to indent using a
tab character instead of 4 spaces.

It also moves around some stuff in .vimrc.after, but it's just
organizational changes and changes to comments.
Add ~/.js to repo, containing GitHub TOC script

We now track "dotjs" scripts in the ~/js directory.

At present, there is one script: it adds a TOC to GitHub pages which
contain MarkDown content.