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            |

features/steps/coverage_extras_steps.py

@@ -90,16 +90,12 @@ def step_test_empty_inits(context):
     modules_to_test = [
         "cleveragents.application",
         "cleveragents.application.services",
-        "cleveragents.application.workflows",
         "cleveragents.cli.commands",
         "cleveragents.domain",
         "cleveragents.domain.contexts",
         "cleveragents.domain.models",
-        "cleveragents.domain.plans",
-        "cleveragents.domain.repositories",
         "cleveragents.infrastructure",
         "cleveragents.providers",
-        "cleveragents.runtime",
         "cleveragents.shared",
     ]
 

features/steps/module_coverage_steps.py

@@ -78,7 +78,6 @@ def step_import_all_modules(context):
         "cleveragents",
         "cleveragents.application",
         "cleveragents.application.services",
-        "cleveragents.application.workflows",
         "cleveragents.cli",
         "cleveragents.cli.commands",
         "cleveragents.config",
@@ -86,11 +85,8 @@ def step_import_all_modules(context):
         "cleveragents.domain",
         "cleveragents.domain.contexts",
         "cleveragents.domain.models",
-        "cleveragents.domain.plans",
-        "cleveragents.domain.repositories",
         "cleveragents.infrastructure",
         "cleveragents.providers",
-        "cleveragents.runtime",
         "cleveragents.shared",
     ]
 

robot/architecture.robot

@@ -15,7 +15,6 @@ Package Structure Should Follow Layered Architecture
 
     # Check main packages exist
     Directory Should Exist    ${SRC_DIR}/cli
-    Directory Should Exist    ${SRC_DIR}/runtime
     Directory Should Exist    ${SRC_DIR}/application
     Directory Should Exist    ${SRC_DIR}/domain
     Directory Should Exist    ${SRC_DIR}/infrastructure

src/cleveragents/application/workflows/__init__.py

@@ -1,6 +0,0 @@
-"""Application workflows.
-
-Contains workflow implementations for complex business processes.
-"""
-
-__all__ = []

src/cleveragents/domain/plans/__init__.py

@@ -1,6 +0,0 @@
-"""Plans domain module.
-
-Contains domain models and business logic related to development plans.
-"""
-
-__all__ = []

src/cleveragents/domain/repositories/__init__.py

@@ -1,7 +0,0 @@
-"""Repository interfaces.
-
-Contains abstract repository interfaces that define data access contracts.
-Concrete implementations live in the infrastructure layer.
-"""
-
-__all__ = []

src/cleveragents/runtime/__init__.py

@@ -1,16 +0,0 @@
-"""Runtime Layer - Server and Background Workers.
-
-This layer handles:
-- HTTP/WebSocket server implementation (80 endpoints)
-- Background worker orchestration (61 behaviors)
-- Process lifecycle management
-- Shared DI container configuration
-
-Responsibilities:
-- Start/stop server processes
-- Manage background tasks
-- Handle HTTP/WebSocket requests
-- Coordinate worker lifecycles
-"""
-
-__all__ = []