Well as you know this is ionic project and its not theme which has provisions to update them .
Changes are directly needed to be done in core files in app .
You need to use a diff tool like (kaledioscopde for mac or winmerge for windows ) or subversion control like github or something to track the changes in your and our files .
PS: we use github to keep track of it and pull the changes done .
So you have to create two branches names wplms_app_updated and wplms_app_mine .
Switch to " wplms_app_updated " then download latest source code and update this branch with it while wplms_app_mine branch will hold your current changes .
Then you can switch to wplms_app_mine branch and can pull changes from wplms_app_updated branch .