One of the design goals of msms was to have a code base that can be easily extensible. Contributions means getting familiar with the code, and a good place to start is with the developers documentation. This gives more details about how the code works and how it fits together.
The primary source management tool we use is git, a distributed version control system. This has a number of features that permits easy forking and merging of a project like this. For example, if you want to develop some extensions, you probably want to work on it, get some results and then publish some kind of application note. With git you can keep up to date easily, and once you have the publication ready, you only need to let me know. I can review the changes, and merge the patch incorporating the extension into the core program.
Alternatively, you can use Java's late linking behavior to create an extension that does not even need to be included into the core, but by simply specifying some special command line options.