I've found an odd quirk/bug with CKAN that I'm not sure is intentional or not. I was manually installing a few mods that have yet to update their DL locations after Kerbalstuff's shutdown, but after installing them CKAN suddenly stopped recognizing my modded KSP folder as a valid install. After a little bit of testing, I figured out that overwriting the readme.txt in the main folder was the cause, and that restoring the original readme.txt fixed it.