We moved from a hosted Windows server to a dedicated Linux server today.

Everything copied as expected, all plugins work, except RaidableBases.  There are no errors, but no bases are spawned, and attempting to use /rbe results in an error about no bases being configured.

After some digging around, I decided to move one base from the subdirectory we keep them in, into the root of copypaste, and update the appropriate profile entry.  That base now works.

Attempting to change the path to copypaste/remaining/path/to/base.json   or ./path/to/base.json    does not. work.   Using ./ results in an error about going outside the oxide directory (seems to be stripping the period), and using copypaste just results in 'copypaste/path/to/base trying to paste at xyz"

I can move all the bases to the root of copypaste, but that's going to make a mess, and the current config worked on Windows.   Any help would be appreciated.

You cannot safely do that.... traversing directories like that is very very problemitic...
you only need the reference to move and you have a major problem...
and don't even get me started with   "rm/cp/mv" with such dangerous path configs...

Ensure you have the correct  format for your directory structure  & case is CORRECT!!!
and rights are corectly set.

plugin: oxide/plugins/CopyPaste.cs
config: oxide/config/CopyPaste.json
data is not in  :  oxide/data/  (nothing here!!!)
its here :         oxide/data/copypaste     (inconsistent naming of directory compared to plugin)