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"is there a system file and link checker that will clean the install?"
The first thing to do is to rebuild your rpm data base to make sure it is not corrupted:
I don't know of a command that will magically clean the install. apt-get might do it and then again apt-get might get part way through the job and blow up. You can use the rpm verify option to check the packages that you suspect are corrupt. You can get a list of every package on your system with:
rpm -qa | sort | less
Then you can check the ones that you may have messed up (using gimp as an example) with:
rpm -V gimp
When everything is OK rpm -V gives no messages. If you get a message then there is an error in that package's installation. You can straighten out the messed up packages by using the rpm --force option (using gimp as an example):
However if the problem is mismatched version numbers among the dependencies then using --force immediately is a bad idea. If you have mismatched version numbers then find all of the mismatches and write them down. Decide what versions of which packages you need and then install the correct version of each package over the incorrect version using --force.