Does jEdit preserve file ownership and permissions when it saves files?
One reason this can be an issue is that by default, jEdit adopts the conservative approach of saving a file to a temporary name before renaming that file to the desired name. This procedure minimizes the risk of crashes causing loss of data, and works without reported problems on local file systems. However, when files are served remotely by FTP, Samba or other means, it may not be possible to preserve file attributes on the server because the newly created temporary file’s owner may differ from the owner of the original file on the server. To avoid this problem, you can disable the two-step file saving routine. Select Utilities>Global Options, then under Loading & Saving, clear the checkbox for Two-stage save.