You don't want myFile.cs~ littering up your file system. There are some really heavy-handed fixes out there (like deleting all the files ending in tilde every so often), but that's a far cry from a best practice. In vim, I just set up a backup directory for those files so that they're all in one place, not over the file system. I think that causes some trouble when I edit files of the same name, but I haven't really checked. Still, a much more elegant solution than combing the whole system to blast every backup.

But how to do this in JEdit? Here we go...

Saving Files:

The behavior of the backup feature is specified in the Autosave and Backup pane of the Utilities>Global Options dialog box; see the section called “The Saving and Backup Pane”.`

The default behavior is to back up the original contents to the buffer's file name suffixed with a tilde (“~”). For example, a file named paper.tex is backed up to paper.tex~.
* If the Backup directory setting is non-empty, backups are saved in that location (with the full path to the original file under it). Otherwise, they are saved in the same directory as the original file. The latter is the default behavior.

So on a Mac, that's a Cmd-, for Preferences, then the below...

Step 3.) Profit.

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