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Remove pacman upgrade; Cli options

SamwiseFilmore requested to merge mggmuggins/fix_bootstrap_final into master

Just replaced !1221 (merged) to fix the git mess, these should be all the changes that were reflected over there.

Commit Message:

The script shouldn't upgrade a system, period, see my comments. I also added a cli option to run the bootstrap with an update of the git stuff and run rustup, plus a help flag and the statusCheck.

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