overlay.py: adds update() function

To update local database and overlay source urls, this function
has been created to allow the overlay.type functions to update
their source urls in their own methods.
git.py: moves fix_git_source() function

This function will also be used by the git update() function
that will be added.
git.py: adds update() function

This function will call git remote set-url, replacing the old url
with the new provided by overlay.update().
db.py: adds update() function
api.py: incorporates db.update() in api.sync()