Is there any need for having the versions.txt and changelog files in the final jar?
Since they are in the buildcraft_resources folder they get injected into the jar, so if moved out of the folder and into let's say a versioning folder at the root, version checks will still work (if link in source is changed though).

What's wrong with including the changelog in the final jar?

As @psxlover, I see no point in removing them from the jar. It'll just be disturbing to the version checking system.

Generally speaking, these features are not eligible to be disused here before having been submitted on http://mod-buildcraft.com/forums/index.php?board=4.0.