- Track level of packages properly, they're not level 0 anymore (this
  could yield an issue where a src dep takes precedence over a pkg dep)
- Proper stable sort of vertices in the digraph module
- PkgDeps no longer 'see themselves' when fetching and upgrading after
  locking themselves
- Pkg Locks are added to pkg deps rather than source deps
- Updating test cases to support pkg mocking on top of src mocking

Apps that are no longer used are not automatically deleted, but we tell
users it can be done. This is safer while we're not sure of the
correctness of these messages.

Error messages are added for transient dependencies and dependencies not
found.

- Many apps is supported through and through
- Not mentioning any app upgrades all apps
- Locks are refreshed on disk and tested as such after an upgrade

todo:
- relock stuff
- default to all apps needing upgrade
- more tests?
- pkgs?

Only the most complex case is failing, where cross-dependencies would
need to be refetched as an update clears an app of its dependencies and
a different subtree should override it.

The problem with the current effort is handling of transitive dependency
upgrades and possible values.

Test that all the correct locks are set for an upgrade run.

Now to actually re-run the install deps and prove it works