command.py: better support for subcommands w.r.t. `help`

We can now do e.g. 'chimi help job run' (which is *about* to exist...)
command.py: add command declarations for the job-management API
command.py: re-enabled `fetch_sources` ("fetch")
add git integration, incomplete branch tracking for builds
command.py: section options to the "build" command
command.py/bootstrap(): set save_flag on the package set before saving
core.py: some error classes that should have been in @09f56cf