same method, but with UltraCompare works for me. i use the 'Merge' feature a lot, so as to not have to even copy/paste or dice/splice.
also, i try to comment blocks of code where i have a mod with '// SD - Mod: xxxx' in php and {* SD - Mod: xxxx *} in the tpls.
then a simple grep piped to a txt file, where i use a macro to transform it to a csv for excel to be used as a checklist. (this is extra, but i'm a little anal so what the hell)
