This probably is what it says it is - there are files and/or directories missing from the disk.
Have a look in the Admin -> System info page to see what your "Jira Home" directory is, if you don't already know, then log into the server and check that in that directory, there is a "caches" directory. If there is not, then create one for it.
You should also check the ownership of Jira home and all its subdirectories and files - they should belong to the account that Jira runs as. (Actually, you don't really need to check all of them, on Unix-like systems, you can just issue the fix command of "chown -R jira:jira" assuming the account is called jira)
Once you have made sure the right directory is there and owned by the right user, restart Jira and try a full re-index (not background).
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