Bootstrap.sh: fix formatting; PATH vuln fix; fix args

Replaced tabs with spaces, made all the cli args use getopts, and fixed a nasty $PATH vulnerability. Planning to do more work here in order to remove the system updates from the OS specific functions, but I wanted to split up the commits so that theses changes can be merged even if those aren't.

Why I want to remove system updates: Basically, it seems really out of scope for a script that just installs a few things. The package manager on a system should have its own state figured out and be able to install packages without updates or give appropriate error messages.