The 5.0 builds of jEdit do not replace text correctly when using the Search And Replace dialog - Replace All in directory.
It used to be that all occurrences in the files of given directory were replaced and files where replacement happened opened if they were not open before.
Now the find function works ok, the hypersearch table lists all files and occurrences found, but when using Replace All, the replacement happens only in the current buffer - if it is in target directory. The rest remain unchanged.
The XSearch plugin behaves like this too.