OMG. You offer blind-fix for problems? Good it's not Nuclear plant firmware
Never ever do this if you want quality software. Everything which can be automatically solved is already solved by git. Everything else should be manually examined before commit.
Git is more strict than patch app while cherry-picking, so it may produce such false-conflicts. In this case i suggest to make format-patch and then apply it through patch app. This way is also "automatic" conflict fixer, but in more proper (read: more success chances) way. This will eliminate false-conflicts and will adjust patch lines where possible, although you won't be able to use 3-way mergetool option (which you won't use anyway according to OP).
Samsung Galaxy S4 SHV-E330S: Optimus ROM (TW 4.4.2) & Kernel. CPU OC 2.7GHz, GPU OC 645MHz, non-KNOX bootloader, UHD/SM/360 Camera.
Samsung Galaxy S4 GT-I9500: Optimus ROM (TW 4.4.2), Perseus Kernel. CPU No-OC, GPU OC 700MHz, non-KNOX bootloader.
Past models: Samsung Galaxy SIII SHV-E210K & GT-I9300, Samsung Galaxy SII GT-I9100.