#####[Updating the Applications menu]#####

JWM
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1. In a terminal, run 'fixmenus'
2. Restart JWM

XFCE
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XFCE updates its applications menu automatically, but it may take a few seconds.

CLIMax
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This would have to be done manually to the BASH script itself. There are some
programs that when installed also include a .desktop file with the Category set
to "ConsoleOnly," but not many and having each and every command-line program
adhere to this standard would be the only way to even begin to think about
having CLIMax add items automatically for you.