docs: revise thesis narrative, diagrams, and build layout

tests/docs/test_big_doc_links.py

@@ -25,9 +25,7 @@ def test_big_doc_links_case_study_and_embeds_evidence_index() -> None:
     assert any(link.startswith("../../examples/report_workflow") for link in links)
     assert re.search(r"^# Evidence Index$", doc, flags=re.MULTILINE)
     assert re.search(r"^## Core Workflow Lifecycle$", doc, flags=re.MULTILINE)
-    assert re.search(
-        r"^## Agent Challenge Evaluation Protocol$", doc, flags=re.MULTILINE
-    )
+    assert re.search(r"^## Current Evaluation Boundaries$", doc, flags=re.MULTILINE)
 
 
 def test_project_map_links_big_doc() -> None:
@@ -60,22 +58,19 @@ def test_big_doc_keeps_mcp_as_source_family() -> None:
     assert "product identity" in doc
 
 
-def test_thesis_has_no_placeholder_author_and_keeps_appendix_evidence_together() -> (
-    None
-):
+def test_thesis_retires_campaign_without_removing_historical_evidence() -> None:
     doc = (ROOT / "docs" / "thesis" / "system-design-implementation.md").read_text(
         encoding="utf-8"
     )
-    appendix = doc.split("# Agent Challenge Harness", maxsplit=1)[1]
-    figure = appendix.index("#fig:agent-challenge-audit")
-    evidence = appendix.index("Evidence:")
-    page_break = appendix.index("\\clearpage")
-
     assert 'author: "draft"' not in doc
     assert "This draft includes" not in doc
-    assert page_break < evidence < figure
-    assert figure > evidence
-    assert 'latex-placement="H"' in appendix[figure : figure + 300]
+    assert "# Agent Challenge Harness" not in doc
+    assert "36-trial" not in doc
+    assert "36 audited trials" not in doc
+    archive = ROOT / "docs/historical/thesis/2026-09-07-retired-agent-evaluation.md"
+    historical = archive.read_text(encoding="utf-8")
+    assert "# Agent Challenge Harness" in historical
+    assert "36" in historical
 
 
 def test_thesis_bundle_has_reproducible_agent_evaluation_assets() -> None:
@@ -94,7 +89,7 @@ def test_thesis_bundle_has_reproducible_agent_evaluation_assets() -> None:
 
     assert (thesis / "agent-challenge-cohort.json").is_file()
     assert (thesis / "agent-challenge-results.md").is_file()
-    assert "include-agent-challenge-results" in doc
+    assert "include-agent-challenge-results" not in doc
     assert "include-markdown.lua" in generate_script
     assert "figure-format.lua" in generate_script
     assert "thesisFigureFormat" in generate_script