add the --no-color and --no-progress flags to the common options setup

This fixes calling bootstrap with these options (as CI servers
do)
bootstrap: do not run an update-config in autoproj-bootstrap

This breaks non-interactive builds as we usually inject the
config.yml file between the bootstrap and the update.
cache: ignore initial checkout errors when running with -k

The normal autoproj behaviour is to never ignore checkout errors
(as one cannot build if no version of the code is there). However,
in the caching case it is harmless to continue, so do ignore
those as well.
make update-config also update autoproj itself
bootstrap: interpret the AUTOPROJ_USE_PRERELEASE envvar as if 'dev' was given on the command line

This is for consistency reasons, as the main autoproj tool understands
the envvar.
re-add Manifest#each_package for backward compatibility reasons
generate autoproj_bootstrap
fix issues with SHELL not being the current shell

This commit makes the shell helpers file portable, and loads it
regardless of the current shell. Since env.sh can really only be
loaded on a bourne-like shell, this is not an issue

Tested on dash, bash and zsh