(PUP-2936) Fix checksum during PMT build

Prior to this commit `puppet module build` was checksumming the source directory
and putting that in checksums.json.
This commit corrects that behavior so it checksums the built module instead.
(PUP-2936) Add warning for 'checksums'

This commit adds a warning to `puppet module build` when it finds a 'checksums'
field in metadata.json. This was done to make people aware of the fact the field
is deprecated and will not be used by the builder, although the installer/upgrader
and other module tools will use the field if checksums.json is not present.
Merge pull request #2897 from highb/fix/stable/pup-2936_pmt_checksums

(PUP-2936) Fix checksum during PMT build (stable branch)
(maint) enable 'add_el_extras' for Beaker

Internally, we removed EPEL repos from our acceptance VM templates.
We found that, for our testing to be successful, we have a package
or two that comes from EPEL. This commit sets 'add_el_extras' to 'true'
so that Beaker can setup the EPEL repos on a SUT.
Merge pull request #2906 from rji/maint/stable/add_el_extras

(maint) enable 'add_el_extras' for Beaker
Merge branch 'stable'