This scenario occurs when Paper-API fails, we then rebuild the patches,
however Paper-Server was left un an outdated state since the most
recent patches did not get applied to it.
This results in us reverting Paper-Server to an older state.
If Paper-API fails to apply, then Paper-Server has to be considered dirty.
This should avoid us having accidental patch reversions
Instead of checking whether it was set previously, setting it to false,
then setting it back to true if it was true before, just use the
command-line argument in git to override the config for that command.
Using a variable makes it pretty painless to do.
