Fixes#9840
The new apply graph wasn't properly nesting provisioners. This resulted
in reading the provisioners being nil on apply in the shadow graph which
caused the crash in the above issue.
The actual cause of this is that the new graphs we're moving towards do
not have any "flattening" (they are flat to begin with): all modules are
in the root graph from the beginning of construction versus building a
number of different graphs and flattening them. The transform that adds
the provisioners wasn't modified to handle already-flat graphs and so
was only adding provisioners to the root module, not children.
The change modifies the `MissingProvisionerTransformer` (primarily) to
support already-flat graphs and add provisioners for all module levels.
Tests are there to cover this as well.
**NOTE:** This PR focuses on fixing that specific issue. I'm going to follow up
this PR with another PR that is more focused on being robust against
crashing (more nil checks, recover() for shadow graph, etc.). In the
interest of focus and keeping a PR reviewable this focuses only on the
issue itself.
