Moving JS files to the right place

The live file should go in the vendor folder since it is a 3rd party
module.

The main.js file was the old pre-backbone way of doing things. I've
removed this and replaced it with the new backbone js.

Updated the HTML to reflect new paths.
Only use the local jQuery
Switching from tabs to spaces

I had something borked in my Vim config and was adding spaces instead of
tabs. Fixed everywhere.
Fixing leading zero on a number
Removing unused colorModifier var
Style improvements

No functional changes. Just style suggestions from JSLint.
Removing stray debug code
Cleaning up map var usage
Removing unused variables.
Simplifying further

We don't need a variable if it's only used once.
Remove dollar sign form variable name

People use this to denote variables that contain jQuery objects, but I'm
not using this convention anywhere else, so I wanted to remove it here
to avoid confusion.
Better comments
Adding standard timescale colors

These colors are based on the standards established by the Commision for
the Geological Map of the World.

I am removing the dynamic color generating code, since these colors are
hand added to match the time period.

I also have some time period name fix in here based on looking at the
current names.
Better style for the active era highlighter

More subtle
Slight style adjustment
Merge branch 'js-refactor'

Cleaned up the JS and moved some things around to improve code quality.