docs(thesis): reconcile scheduling evidence and remove orphaned paragraph

docs/thesis/system-design-implementation.md

@@ -519,10 +519,9 @@ records. An external agent can use the same client operations. Evaluating these
 interfaces requires observing how authors discover operations, repair
 definitions, and interpret results.
 
-Model Context Protocol (MCP) supplies another part of the integration: access
-to tools, resources, and prompts [@mcp-tools-2025; @mcp-lifecycle-2025]. A
-configured MCP source can supply operations and readable content. The workflow
-runtime determines routing and state updates independently of that protocol.
+A configured Model Context Protocol (MCP) source supplies operations and
+readable content; the workflow runtime determines routing and state updates
+[@mcp-tools-2025; @mcp-lifecycle-2025].
 
 # Conceptual Model
 
@@ -1710,8 +1709,8 @@ deployment, execution,
 refresh, and trace inspection, while excluding network startup and transport
 behavior from the observation.
 
-[@tbl:prototype-conformance] records the concrete checks performed by that
-session. The fixture expectations are fixed independently of the workflow's
+[@tbl:prototype-conformance] records the requirement-linked checks performed
+by that session. The fixture expectations are fixed independently of the workflow's
 result, and stored output is inspected again through the API.
 
 | Check | Expected observation | Requirement |
@@ -2004,13 +2003,15 @@ all listed suites passed in one newly recorded full-system run.
 
 ## Core workflow lifecycle
 
-**E1**: artifacts, deployments, stopped runs, and explicit resume boundaries.
+**E1**: artifacts, deployments, scheduled execution, stopped runs, and explicit
+resume boundaries.
 
 - `src/wf_artifacts/models.py`
 - `src/wf_artifacts/runs/`
 - `src/wf_api/run_lifecycle.py`
 - `tests/wf_api/test_artifact_api.py`
 - `tests/wf_api/test_run_api.py`
+- `tests/examples/test_scheduled_deployment_example.py`
 
 ## Python authoring and inspection