Remove Makefile from Git. It is generated during the install process
Update dependancies
Make admining tags easier by showing the list of documents associated with them.
Better homepage URLs
Quickly remove tags which don't have many documents associated with them.
Don't track inc modules, they are generated.
Have a simple site map

This is mostly so I can quickly get at every document with a link checker :)
Updated meta
Ignore more files
Find links that are going to break during the import
Replace URLs for moved scripts