Add base64 and csv gems to Gemfile

[MikeMcQuaid]

These will be needed with Ruby 3.4 and base64 is blocking #16893.

Relatedly:

• don't use HOMEBREW_BOOTSNAP by default in all CI jobs. We can add it back one-by-one where necessary but as-is it's breaking too much with base64
• ensure that csv gem is not committed and optionally installed on demand by brew contributions --csv
• no longer hide warnings about base64/csv requires
• don't run bundle clean because it can remove gems we need