I figured this out. I upgraded last month and a few repository folders somehow did not copy to the location were I did the update. Copying the missing folders in did not work. I ended up copying the backup I did to another server and installing the old version on there then doing the update again. Luckily we did not make any changes on any of the older repositories sense the update just added two new ones. I just imported them to the server I redid the update on. After I did that I just moved it back to the first server.
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