diff --git a/features/architecture.feature b/features/architecture.feature
index d0cd81f43..3c11e38ef 100644
--- a/features/architecture.feature
+++ b/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            |
diff --git a/features/steps/coverage_extras_steps.py b/features/steps/coverage_extras_steps.py
index 0abe065fc..9cd04bc21 100644
--- a/features/steps/coverage_extras_steps.py
+++ b/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",
     ]
 
diff --git a/features/steps/module_coverage_steps.py b/features/steps/module_coverage_steps.py
index 82928fc19..36aa48a28 100644
--- a/features/steps/module_coverage_steps.py
+++ b/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",
     ]
 
diff --git a/robot/architecture.robot b/robot/architecture.robot
index 9d9261809..0d21607ea 100644
--- a/robot/architecture.robot
+++ b/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
diff --git a/src/cleveragents/application/workflows/__init__.py b/src/cleveragents/application/workflows/__init__.py
deleted file mode 100644
index 20e678484..000000000
--- a/src/cleveragents/application/workflows/__init__.py
+++ /dev/null
@@ -1,6 +0,0 @@
-"""Application workflows.
-
-Contains workflow implementations for complex business processes.
-"""
-
-__all__ = []
diff --git a/src/cleveragents/domain/plans/__init__.py b/src/cleveragents/domain/plans/__init__.py
deleted file mode 100644
index 908ea5c7d..000000000
--- a/src/cleveragents/domain/plans/__init__.py
+++ /dev/null
@@ -1,6 +0,0 @@
-"""Plans domain module.
-
-Contains domain models and business logic related to development plans.
-"""
-
-__all__ = []
diff --git a/src/cleveragents/domain/repositories/__init__.py b/src/cleveragents/domain/repositories/__init__.py
deleted file mode 100644
index aeb287540..000000000
--- a/src/cleveragents/domain/repositories/__init__.py
+++ /dev/null
@@ -1,7 +0,0 @@
-"""Repository interfaces.
-
-Contains abstract repository interfaces that define data access contracts.
-Concrete implementations live in the infrastructure layer.
-"""
-
-__all__ = []
diff --git a/src/cleveragents/runtime/__init__.py b/src/cleveragents/runtime/__init__.py
deleted file mode 100644
index 18af35e19..000000000
--- a/src/cleveragents/runtime/__init__.py
+++ /dev/null
@@ -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__ = []