Show the "extracted" state of the file scopes in "machinery show"

Fixes #254
DRY incompatible description errors into SystemDescriptionIncompatible

The same error message was used several times across the source code. It
is now extracted into a specific exception class for that case.

Fixes #257
Handle upgrade failures and continue in "machinery upgrade-format --all"

Fixes #256
Fixes #258
Write information about description upgrades to the machinery log

Fixes #259
Improve machinery output in "machinery upgrade-format"