Drop support for --packages-dir flag (#1958)

Towards #1952

Drops support for the flag and updates tests that were depending on it
or referring to it, but does not remove the supporting code. That will
be done in a followup.

- Parse but ignore the flag and warn when it is used.
- Drop tests specifically for the packages dir behavior.
- Remove unnecessary references to the flag.
- Drop utility test code and constants for the packages dir.
- Wherever possible replace checks for content within the packages dir
  with checks for content in the package spec, and sometimes cache.
- When working with git shas which are unpredictable and have an ugly
  format in the package spec check instead for lines that contain the
  sha, or which have a package spec which either specificially did or
  did not change after an upgrade.