Update packages.yaml format and support configuration updates

The YAML config for paths and modules of external packages has
changed: the new format allows a single spec to load multiple
modules. Spack will automatically convert from the old format
when reading the configs (the updates do not add new essential
properties, so this change in Spack is backwards-compatible).

With this update, Spack cannot modify existing configs/environments
without updating them (e.g. “spack config add” will fail if the
configuration is in a format that predates this PR). The user is
prompted to do this explicitly and commands are provided. All
config scopes can be updated at once. Each environment must be
updated one at a time.