I have a application running that is causing errors when I reboot or shutdown the computer... as it is not closing correctly. Basically the computer is rebooting before it finishes closing down.

I thought I could edit a .desktop file for reboot and shutdown to run a script rather than whatever it is doing right now and that script will use the command line to shutdown my app correctly, pause and then reboot or poweroff the computer.

I can not seem to find that file.

TL;DR : How can I edit the menu item in system for reboot and shutdown to run a script instead of just shutting or rebooting normally? Also when I type reboot or shutdown in the terminal, is there a way I can make that also run the same script?

Pretty sure shutdown from bodhi executes shutdown, reboot executes reboot. No desktop files involved, although you certainly could make them, and have them call a script that does whatever you want before shutdown now.

What's actually happening? I thought shutdown gives an app like 2 minutes to shutdown before it kills it... I guess if yer app isn't ever closing when told and you know its safe to kill you could do as I just typed and make your script kill it first.

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This really needs to be looked at closer.
PLease clarify.

edit: see here.

BTW, it's does, not dose (seen you misspelling that a few times now).

It is apparently a known bug in cryptomator at the mo. It is supposed to close the vaults on shutdown of the app, but unless you manually shutdown it dose not happen. I think they are going to try and fix it. It dose bug me but I am pretty sure that I can live with it and wait for an update. Even so, it would be cool to know if this is possible.

Just to refresh...

I am trying to replace the MENU item in BodHi for "shutdown" and "reboot" to run a script instead of doing w/e it is normally doing.