Modules that replace the same file

[hawaii350]

As I'm sure you are aware there are a lot of modules or modifications out there that do not install via the backoffice and instead require you to manually install them. The problem here is a lot of these modify the same files. I've tried to use winmerge but since I did not write the code its hard to figure out what parts to merge and what to get rid of not to mention some modify the same line of code in a different way.

Is there any simple way of making these modules work together