Once having compiled the Android project, it will have output stuff into local bin/ folders etc. This causes a problem with source repos since that would add all those unnecessary binaries to the repo. How do we clean the project folder (with the cocos command?)
And/or preferably have the cocos run command compile stuff into an outside temporary folder - how?
instead of deleting the binary stuff, you should add these files to .gitignore or equivalent if you are not using git.
Yes so how do I know what files should be ignored? I normally use SVN. I randomly exclude bin, gen, libs and some more for now. (forgot)… I think it would be very useful to explicitly list these somewhere… or put all products inside just one temp folder, maybe outside source directory. Like Xcode does 
You can use cocos2d-x .gitignore as a starter point (though it will probably be over-broad for your app): https://github.com/cocos2d/cocos2d-x/blob/v3/.gitignore
It is up to you to know your build system, and what files are generated and can be safely ignored from you control-version system.