Hi Shao,
the first thing you need to take into account is that we use "gulp" to build the Javascript file.
If you have your environment ready to use gulp (as it is explained in here) you can edit the files inside www/addons and www/core to achieve what you want. You should open www/addons/files/main.js and delete the line:
$mmSideMenuDelegateProvider.registerNavHandler('mmaFiles', '$mmaFilesHandlers.sideMenuNav', mmaFilesPriority);
You need to run gulp after applying these changes. This will remove the My Files option.
If you don't, then you'll have to edit www/build/mm.bundle.js. You need to delete the same line as above. In this case you don't need to run gulp since you're already editing the final file.
Please let me know if you have any other problem.
Cheers,
Dani