We have made no changes to the https://github.com/openworm/segworm repository. It is there as a record of the work you did at the Schafer Lab. If you want to make commits to that, please feel free, it is your codebase :)
Since August 2013 Jim and I and others have ported the SegWorm code to Python and made numerous structural changes and improvements. That is now called the "OpenWorm Analysis Toolbox", and it's being used by OpenWorm and André Brown in their respective analysis pipelines. So depending on the kind of changes you want to commit, it may make sense to also create an issue at the https://github.com/openworm/open-worm-analysis-toolbox repository requesting to port your new code.
Hope this helps!