When using jedit to edit files that will be saved on a remote linux or unix system, you may run into problems if you don’t change the code jedit puts at the end of the line to indicate a return. Jedit calles this the default line separator.
There are two ways to change the default line separator. Which way you choose depends on how you use jedit. If you only use jedit to edit files on a Unix or Linux system then make the change to the global jedit settings and never think about it again. If you use jedit for other editing as well, you may want to change the the line separator on a case by case (or in jedit terms, buffer by buffer) basis. Changing the global defalt is a one time thing. If you leave the global defalt on a setting other than Unix you need to remember to change the Buffer Options each time you want to edit a file for use on the remote Linux system.
To change the global options, select Utilities→Global Options→Default Line Separator→Unix
Once you have made the change to Unix click on OK. From that point on any new files should use the correct default setting. Note: This will not change a file that you have open when you make this change. To change an open file you must change the Buffer Options.
If you want to change the line separator for a particular buffer, you do that by selecting Utilities→Buffer Options→Default Line Separator→Unix
Some folks using jedit on the windows machines to edit files on a remote linux system have reported that it seems to be remembering their linux passwords. If this happens to you, then you can tell jedit to forget any passwords it has captured with:
Plugins–>FTP–>Forget Remote Passwords
— Greg Priest-Dorman 2008/09/08 15:18