So your choices are running JD from IDE will mean no updates from update network and also means IDE has to be open. If you want to still run public BETA (has some benefits like Container support and updates), you will need to make your changes for personal use by, copying existing class (give it a new name) and change the interface level + 1 (JD will load the highest interface level). Copy over the new class files to your standalone version (require shutting down, copying class', and restarting). Doing this will mean you will need to maintain updates to those custom plugins as they are now a new class and higher interface.
re: GIT
Since you need to sign your life away before adopting users code to JD repositories, Appwork wont merge users code without that agreement. Supplying outside of having SVN access can be done easily enough via submitting a patch (under team right click context > create patch). I don't see Appwork changing to GIT anytime soon, it's been discussed before (in our development channel).
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