I was diffing those ancient Bugzilla modifications that I did not introduce myself under /template/en/custom/global.

code-error.html.tmpl
Only the line "[%# style changed --pdhanda #%]" seems to be a relevant customization, and not worth keeping.

header.html.tmpl
A bunch of "Wikimedia skin" changes (like bodyclasses = ['skin-vector']) here.
Upstream rev7610 is still included, but everything from rev7733 on (and until 4.2) should get integrated as there are actual bug fixes, see
http://bzr.mozilla.org/bugzilla/trunk/changes?filter_file_id=header.html.tmpl-20070302081301-38udvt2x2mjyllig-811

site-navigation.html.tmpl
File is identical to /default and can be removed.

Version: wmf-deployment
Severity: minor