Is it not easier to just make an object which handles all the talking from/with the FTP from within your main app?
Certainly not. I'm not reinventing FTP when someone else has made a perfectly good library for it.

Or perhaps you mean to have the FTP commands in my java code, which I do. The command line (and thus, the batch file) takes a single parameter, and that's whether to do a validation (no option) or create a checklist (added createlist).

What is my batch file, if not this shortcut you propose? I'm the only one who probably ever need to run it in the mode to create a list anyway.

I tried to run it as an executable jar, and it seems to remove the DOS window that is required for the simple user input when running (which checklist to download), without making it into a swing application. I'm not doing this.