refactor(cleanup): remove or implement empty stub packages

Remove four empty stub packages that contained only __init__.py with
__all__ = [] and no functional code, violating CONTRIBUTING.md §Commit
Completeness. All four were audited against docs/specification.md:

- src/cleveragents/runtime/ — Spec defines four layers (Domain,
  Application, Infrastructure, Presentation) with no Runtime Layer.
  Runtime concepts (LSP Runtime, actor runtime) belong in Infrastructure.
- src/cleveragents/domain/repositories/ — Spec mentions repository
  interfaces in Domain but mandates no separate subpackage. Empty with
  no protocols defined; existing models cover the domain.
- src/cleveragents/domain/plans/ — Plan domain models already exist in
  domain/models/planconfig, planfiles, and plansettings. Empty duplicate.
- src/cleveragents/application/workflows/ — Application logic already
  served by application/services/. Empty stub added no value.

Updated test references in features/steps/module_coverage_steps.py,
features/steps/coverage_extras_steps.py, features/architecture.feature,
and robot/architecture.robot to remove the deleted packages from import
verification and architecture validation lists.

ISSUES CLOSED: #948

Co-authored-by: Brent E. Edwards <brent.edwards@cleverthis.com>
Co-committed-by: Brent E. Edwards <brent.edwards@cleverthis.com>

features/architecture.feature

@@ -13,7 +13,6 @@ Feature: Architecture validation
     Then I should find these main packages:
       | package          | description                      |
       | cli              | Command line interface           |
-      | runtime          | Server and background workers    |
       | application      | Business logic and workflows     |
       | domain           | Domain models and contracts      |
       | infrastructure   | External integrations            |