When you say "by-hand"... the times I've checked, I haven't seen a "make uninstall" target for the modules I've installed. Is that common (to not have an uninstall target)? If so, how do you uninstall?
Uninstalling by hand means going to you lib/perl5/ and deleting the files. This can be dangerous, but if you take care it's easy and quick. But my main point was don't worry too much about uninstalling modules.
But, when you say you "install by-hand", does that mean you go to where CPAN.pm downloaded the source files (umm... maybe somewhere in /root/.cpan?) and run "perl Makefile.PL..."? Or do you download a fresh archive?
I download a fresh tarball from CPAN and extract (not that it should make a big difference from the .cpan). Then perl Makefile.PL
(or Build.PL depending) -> make
-> make test
-> su -c 'make install'
So, how exactly do you "upgrade by-hand" if you've already got the previous version installed? If I were going from using a 1.x to a 2.x, I'd want to make sure all the 1.x files were completely removed first, right?
Unless specified by the POD documentation you shouldn't have to worry about removing old modules. They should be overwritten. After install hundreds of modules I can't think of any real upgrade weirdness other than once with a big update to Class::DBI. But since I generally do upgrades one-at-a-time, it was easy to find out where to update my code.
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