Apache with mod_perl 2.0.1-r2 is prevented from loading after perl-cleaner is run, because the required ModPerl/Util.pm has moved, or something has changed the apache2-mod_perl-startup.pl @INC variable to exclude its search path. Therefore, I have added an include statement for it, and am posting a patch.
Created attachment 89685 [details, diff] A patch which updates the @INC in the aforementioned perl script A GPG signature is attached.
Created attachment 89686 [details] The signature to the patch I proposed.
Well no, this fix is wrong, you cannot hardcode versions there, and you cannot hardcode threaded/non-threaded there... Wouldn't work on my system, e.g. Also, mod_perl works just fine here, I' say your problem is somewhere else.
Tried reemerging mod_perl?
If you upgrade perl, you have to rebuild mod_perl. It links and builds based on the system libperl, so if that changes you need to reinstall. FWIW, you also must rebuild if you change from using ithreads to not (or vice versa).
After remerging mod_perl, everything works again.