I just solved this myself by:
git checkout -b tmp # "tmp" or pick a better name for your local changes branch
git add -A
git commit -m 'tmp'
git checkout master # Or whatever branch you were on originally
git diff tmp
where the last command gives a list of what your local changes were. Keep modifying the "tmp" branch until it is acceptable and then merge back onto master with:
git checkout master && git merge tmp
For next time, you can probably handle this in a cleaner way by looking up "git stash branch" though stash is likely to cause you trouble on the first few tries, so do first experiment on a non-critical project...