Update install script

- Update install script with comments
- Create checks for helper files, ensure they are actually sourced
- Remove `run_cli` function as it was no longer necessary; it depends on
  php, so update `run_php` function to include for continuity
- Update all exit statements to send status 1 as that is the accepted
  practice
- Update `link` & `copy` function within /lib/setup to reference correct
  directory/path
- Remove extraneous line breaks in `printf` statements
- Update `change_shell` function; change order of operations since
  /etc/shells needs to be updated before you can actually change to the
  Homebrew shell

Issue: #9