Make sure we don't build the same tools tree more than once

Make sure we don't build the same tools tree more than once

We can do this by simply checking if the output path already exists
instead of relying on needs_build(). This allows us to refactor
needs_build() to needs_clean(). We also move some prechecks into
run_build() and run_clean() so as to not duplicate them and improve
the logging messages in run_clean().

Fixes #2280