Factor out the mechanism for calculating the repo's fileURL

This is the address used to identify an instance of our NSDocument
subclass; for recent lists, etc.
Always use the same URL calculation when storing or comparing fileURL
Stop a crash when opening a bare repo
Update change log
Update to upstream SyntaxHighlighter

n.b. For GitX, this just updates the submodule, it doesn't use the new code yet

It seems there's a critical break in GitX's usage that stops all highlighting from working.