I have a commercial Android project that I have created a client-specific version for (mainly UI tweaks). Since the bulk of the tweaks are in the res/ folder in XML files, we have the changes currently in a branch but I really don't want to have to port changes back and forth between branches in perpetuity. I'm curious if anyone has any source control strategies that will make managing multiple client-specific versions of an Android application as painless as possible.

Also, not sure if this belongs here or StackOverflow. Feel free to transition over there if I guessed wrong.

Security through obfuscation is never good security. There must be better ways of protecting your intellectual property. And that is what you and your colleague should bring up as a joint concern with your manager. If management then decide that they don't want to spend the time or money on improved security, then both of you will have to live with that decision (it's not your product, it's the company's product) and better not spend (waste?) any more time on the subject.