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Problems with Ruby Gems after Rails Upgrade

I recently installed a new ruby application. One of our clients has a production site on our server.
I had to update the client's code to fix some of another developers deprecated code.
I setup apache httpd.conf for the correct virtual host proxy for this site.

I noticed gem wasn't working correctly, due to an issue from upgrading rails on that machine, so I fixed it ( adding require 'rubygems/gem_runner' to /usr/local/bin/gem in the appropriate place ) along with installing the ruby mysql gem ( I did this after getting a warning about the need for the ruby extension for mysql ). There were also some issues inside the application concerning a linux shared object rails extension, so I recompiled that extension in /home/clientdirectory/working/lib/PDFlib.so.

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