I don't think you need to delete your entire config. Most of it should be fine.
But, if some path to old stuff is stored there, one way would be to backup the folder, and restore it file by file to see which file causes any trouble.
Since this is about packages, I suspect:
includelinks.xml
packagefiles.xml
staticpackages.inc
Added AnchorDocking to the list and initiated the package build. Got error in ZDbcCache:
So you got "Zeos" installed.
And the Zeos version you have does not work with the new IDE.
I don't use Zeos myself, but I expect they have a newer version that will work.
If you used OPM, maybe it can be updated via OPM. => I don't know if the OPM registry has the latest updates already included. (Afaik, It is maintained separately from the release).