meld

Both for maintaining github repositories, and assorted code merging, I've been enjoying using the tool "meld". For adhoc merging, if you have two different versions of a file, do

meld [filename1] [filename2]

You'll then see the two files in parallel, with MELD highlighting new, changed or deleted code in each file. You can then click the arrows to transfer the change in one direction or the other.

You may also merge more than two versions.

If you use git, you may set this to use meld by default:

git config --global merge.tool meld

Then type

git mergetool

will resolve all of the conflicts that have arisen with an update.