fix/code fix prompt is self contained

.github/workflows/ci-pipeline.yml

@@ -118,12 +118,12 @@ jobs:
         run: |
           export PYTHONPATH="${PYTHONPATH}:${PWD}"
           python -c "
-          from medharness.workflows.init import _scaffold_dhf
+          from medharness.scaffold import scaffold_dhf
           from pathlib import Path
           import tempfile
           with tempfile.TemporaryDirectory() as tmp:
               dhf_dir = Path(tmp) / 'test-dhf'
-              _scaffold_dhf(dhf_dir)
+              scaffold_dhf(dhf_dir)
               assert (dhf_dir / 'DHF' / 'config' / 'global.yaml').exists()
               assert not (dhf_dir / 'DHF' / 'config' / 'doc_types').exists()  # defaults are inherited
               assert (dhf_dir / 'DHF' / 'items').exists()
@@ -152,13 +152,13 @@ jobs:
         run: |
           export PYTHONPATH="${PYTHONPATH}:${PWD}"
           python -c "
-          from medharness.workflows.init import _scaffold_dhf, _replace_placeholders
+          from medharness.scaffold import scaffold_dhf, replace_placeholders
           from pathlib import Path
           import tempfile, subprocess, sys
           with tempfile.TemporaryDirectory() as tmp:
               dhf_dir = Path(tmp) / 'starter-dhf'
-              _scaffold_dhf(dhf_dir)
-              _replace_placeholders(dhf_dir, 'Test Project')
+              scaffold_dhf(dhf_dir)
+              replace_placeholders(dhf_dir, 'Test Project')
               dhf = str(dhf_dir / 'DHF')
               subprocess.run([sys.executable, '-m', 'medharness', '--dhf', dhf, 'verify', 'dhf'], check=True)
               # The starter items say 'Replace with your own': strict refuses them, so they cannot ship.

CHANGELOG.md

@@ -11,6 +11,21 @@ MedHarness follows [Semantic Versioning](https://semver.org/):
 
 ## [Unreleased]
 
+## [0.54.1] — 2026-10-04
+
+### Fixed
+
+- **The code review's fix pass now carries the issues it must fix.** The prompt said "the review above",
+  which only a model resuming the session could see; a model from another provider (no sessions) was
+  told to fix nothing in particular. The issues are in the prompt.
+- The design review's "already checked" note no longer mentions a spec file that no stage writes.
+
+### Changed
+
+- `medharness/workflows/` is gone: `init.py` is `medharness/scaffold.py` (its test helpers lose the
+  underscore: `scaffold_dhf`, `replace_placeholders`) and `cr_state.py` is `medharness/services/cr_state.py`.
+  Nothing in it was a workflow. No behaviour change.
+
 ## [0.54.0] — 2026-10-04
 
 ### Changed
@@ -2976,7 +2991,7 @@ a compliance record is the defect class that matters most.
 
 ### Internal
 
-- `dhfkit/tests/test_document_generation.py` imported `medharness.workflows.init`,
+- `dhfkit/tests/test_document_generation.py` imported `medharness.scaffold`,
   breaking the `dhfkit` → `medharness` boundary and the ability to run dhfkit's
   suite standalone. It now builds its fixture from the bundled templates
   directly. A check over the whole package confirms no such import remains.

dhfkit/tests/test_cr_closure_criteria.py

@@ -19,7 +19,7 @@
 import pytest
 
 import dhfkit.api as api
-from medharness.workflows.init import _replace_placeholders, _scaffold_dhf
+from medharness.scaffold import replace_placeholders, scaffold_dhf
 
 CLOSURE = {
     "implementation_notes": "Toolbar updated.",
@@ -31,8 +31,8 @@
 
 @pytest.fixture
 def cr(tmp_path: Path) -> tuple[Path, str]:
-    _scaffold_dhf(tmp_path)
-    _replace_placeholders(tmp_path, "Closure")
+    scaffold_dhf(tmp_path)
+    replace_placeholders(tmp_path, "Closure")
     dhf = tmp_path / "DHF"
     for state in ("design", "develop"):
         api.transition_item(dhf, "CR-001", state)

dhfkit/tests/test_dangling_covers_the_schema.py

@@ -26,7 +26,7 @@
 from dhfkit.item_store import ItemStore
 from dhfkit.traceability import find_dangling_links
 from dhfkit.models.config import ProjectConfig
-from medharness.workflows.init import _replace_placeholders, _scaffold_dhf
+from medharness.scaffold import replace_placeholders, scaffold_dhf
 
 TEMPLATES = Path(__file__).resolve().parents[1] / "templates" / "config" / "doc_types"
 
@@ -51,8 +51,8 @@ def test_the_scan_found_fields() -> None:
 
 @pytest.mark.parametrize("field,code", FIELDS, ids=[f for f, _ in FIELDS])
 def test_a_dangling_link_is_detected(field: str, code: str, tmp_path: Path) -> None:
-    _scaffold_dhf(tmp_path)
-    _replace_placeholders(tmp_path, "Dangling")
+    scaffold_dhf(tmp_path)
+    replace_placeholders(tmp_path, "Dangling")
     dhf = tmp_path / "DHF"
 
     target = next(((dhf / "items").rglob(f"{code}-*.yaml")), None)
@@ -78,15 +78,15 @@ def test_a_dangling_link_is_detected(field: str, code: str, tmp_path: Path) -> N
 
 class TestTheFieldSetComesFromTheSchema:
     def test_config_reports_every_declared_relationship(self, tmp_path: Path) -> None:
-        _scaffold_dhf(tmp_path)
-        _replace_placeholders(tmp_path, "Derived")
+        scaffold_dhf(tmp_path)
+        replace_placeholders(tmp_path, "Derived")
         config = ProjectConfig.load(tmp_path / "DHF" / "config")
         assert config.relationship_fields() == {f for f, _ in FIELDS}
 
     def test_a_project_defined_field_is_picked_up(self, tmp_path: Path) -> None:
         """The point of deriving: a field this package has never heard of."""
-        _scaffold_dhf(tmp_path)
-        _replace_placeholders(tmp_path, "Custom")
+        scaffold_dhf(tmp_path)
+        replace_placeholders(tmp_path, "Custom")
         dhf = tmp_path / "DHF"
         from dhfkit.paths import DEFAULT_CONFIG_DIR
 

dhfkit/tests/test_duplicate_item_ids.py

@@ -22,13 +22,13 @@
 
 import dhfkit.api as api
 from dhfkit.item_store import ItemStore
-from medharness.workflows.init import _replace_placeholders, _scaffold_dhf
+from medharness.scaffold import replace_placeholders, scaffold_dhf
 
 
 @pytest.fixture
 def dhf(tmp_path: Path) -> Path:
-    _scaffold_dhf(tmp_path)
-    _replace_placeholders(tmp_path, "Duplicates")
+    scaffold_dhf(tmp_path)
+    replace_placeholders(tmp_path, "Duplicates")
     return tmp_path / "DHF"
 
 

dhfkit/tests/test_ids_are_never_reused.py

@@ -17,7 +17,7 @@
 import pytest
 
 import dhfkit.api as api
-from medharness.workflows.init import _replace_placeholders, _scaffold_dhf
+from medharness.scaffold import replace_placeholders, scaffold_dhf
 
 
 def _git(root: Path, *args: str) -> None:
@@ -31,8 +31,8 @@ def _commit(root: Path, message: str) -> None:
 
 @pytest.fixture
 def repo(tmp_path: Path) -> Path:
-    _scaffold_dhf(tmp_path)
-    _replace_placeholders(tmp_path, "Reuse")
+    scaffold_dhf(tmp_path)
+    replace_placeholders(tmp_path, "Reuse")
     _git(tmp_path, "init", "-q")
     _commit(tmp_path, "scaffold")
     return tmp_path
@@ -81,8 +81,8 @@ def test_ids_are_still_sequential_without_deletions(self, repo: Path) -> None:
 class TestOutsideGit:
     def test_a_dhf_with_no_repository_still_creates_items(self, tmp_path: Path) -> None:
         """History is unavailable there; behave as before rather than fail."""
-        _scaffold_dhf(tmp_path)
-        _replace_placeholders(tmp_path, "NoGit")
+        scaffold_dhf(tmp_path)
+        replace_placeholders(tmp_path, "NoGit")
         dhf = tmp_path / "DHF"
         assert _new_srs(dhf, "a").startswith("SRS-")
         assert _new_srs(dhf, "b").startswith("SRS-")

dhfkit/tests/test_item_writes_are_atomic.py

@@ -22,13 +22,13 @@
 
 import dhfkit.api as api
 from dhfkit.item_store import ItemStore
-from medharness.workflows.init import _replace_placeholders, _scaffold_dhf
+from medharness.scaffold import replace_placeholders, scaffold_dhf
 
 
 @pytest.fixture
 def dhf(tmp_path: Path) -> Path:
-    _scaffold_dhf(tmp_path)
-    _replace_placeholders(tmp_path, "Atomic")
+    scaffold_dhf(tmp_path)
+    replace_placeholders(tmp_path, "Atomic")
     return tmp_path / "DHF"
 
 
@@ -86,8 +86,8 @@ class TestDhfkitDoesNotCommit:
     """
 
     def _repo(self, tmp_path: Path) -> Path:
-        _scaffold_dhf(tmp_path)
-        _replace_placeholders(tmp_path, "Labels")
+        scaffold_dhf(tmp_path)
+        replace_placeholders(tmp_path, "Labels")
         for args in (["init", "-q"], ["add", "-A"],
                      ["-c", "user.email=t@e", "-c", "user.name=t",
                       "commit", "-qm", "scaffold"]):

dhfkit/tests/test_lifecycle_states_resolve.py

@@ -17,7 +17,7 @@
 import yaml
 
 import dhfkit.api as api
-from medharness.workflows.init import _replace_placeholders, _scaffold_dhf
+from medharness.scaffold import replace_placeholders, scaffold_dhf
 
 TEMPLATES = Path(__file__).resolve().parents[1] / "templates" / "config"
 
@@ -59,8 +59,8 @@ class TestTheScaffoldedCRCanReachCompleted:
 
     def test_the_full_path(self, tmp_path: Path) -> None:
         """Closing needs the record that closure is supposed to mean."""
-        _scaffold_dhf(tmp_path)
-        _replace_placeholders(tmp_path, "Lifecycle")
+        scaffold_dhf(tmp_path)
+        replace_placeholders(tmp_path, "Lifecycle")
         dhf = tmp_path / "DHF"
         for state in ("design", "develop"):
             api.transition_item(dhf, "CR-001", state)
@@ -83,22 +83,22 @@ def test_updating_a_field_does_not_undo_the_lifecycle(self, tmp_path: Path) -> N
         Filling in a CR's required fields sent it back to `new`, so the criteria
         above could never be satisfied — the act of qualifying disqualified it.
         """
-        _scaffold_dhf(tmp_path)
-        _replace_placeholders(tmp_path, "Lifecycle")
+        scaffold_dhf(tmp_path)
+        replace_placeholders(tmp_path, "Lifecycle")
         dhf = tmp_path / "DHF"
         api.transition_item(dhf, "CR-001", "design")
         api.update_item(dhf, "CR-001", {"implementation_notes": "x"})
         assert api.get_item(dhf, "CR-001")["status"] == "design"
 
     def test_an_undefined_state_is_still_refused(self, tmp_path: Path) -> None:
         """Widening the state list must not make the machine permissive."""
-        _scaffold_dhf(tmp_path)
-        _replace_placeholders(tmp_path, "Lifecycle")
+        scaffold_dhf(tmp_path)
+        replace_placeholders(tmp_path, "Lifecycle")
         with pytest.raises(ValueError):
             api.transition_item(tmp_path / "DHF", "CR-001", "nonexistent")
 
     def test_skipping_a_state_is_still_refused(self, tmp_path: Path) -> None:
-        _scaffold_dhf(tmp_path)
-        _replace_placeholders(tmp_path, "Lifecycle")
+        scaffold_dhf(tmp_path)
+        replace_placeholders(tmp_path, "Lifecycle")
         with pytest.raises(ValueError):
             api.transition_item(tmp_path / "DHF", "CR-001", "completed")

dhfkit/tests/test_network_calls_have_timeouts.py

@@ -104,7 +104,7 @@ def _text_io_without_encoding() -> list[tuple[str, int, str]]:
 
 
 def test_the_encoding_scan_sees_real_calls() -> None:
-    text = (ROOT / "medharness" / "workflows" / "init.py").read_text(encoding="utf-8")
+    text = (ROOT / "medharness" / "scaffold.py").read_text(encoding="utf-8")
     assert "read_text(" in text, "the probe file no longer does text IO"
 
 

dhfkit/tests/test_stale_global_config.py

@@ -24,16 +24,16 @@
 import yaml
 
 import dhfkit.api as api
-from medharness.workflows.init import _replace_placeholders, _scaffold_dhf
+from medharness.scaffold import replace_placeholders, scaffold_dhf
 
 
 @pytest.fixture
 def aged(tmp_path: Path) -> Path:
     """A DHF whose own lifecycle override predates the states its doc types use."""
     from dhfkit.paths import DEFAULT_CONFIG_DIR
 
-    _scaffold_dhf(tmp_path)
-    _replace_placeholders(tmp_path, "Aged")
+    scaffold_dhf(tmp_path)
+    replace_placeholders(tmp_path, "Aged")
     dhf = tmp_path / "DHF"
     config = dhf / "config" / "global.yaml"
     data = yaml.safe_load(config.read_text())

medharness/cli/build.py

@@ -109,7 +109,7 @@ def change_plan(ctx: click.Context, cr_id: str, pr_number: int | None, since_ref
         pushes to that PR, revising when a reviewer asked for changes.
         """
         from medharness.services.cr_generation import generate_dhf  # noqa: PLC0415
-        from medharness.workflows.cr_state import assert_cr_active  # noqa: PLC0415
+        from medharness.services.cr_state import assert_cr_active  # noqa: PLC0415
         dhf: Path = ctx.obj["dhf"]
         try:
             store = open_store(ctx.obj["dhf"])
@@ -167,7 +167,7 @@ def change_implement(ctx: click.Context, cr_id: str, pr_number: int | None,
         pushes to that PR, revising when a reviewer asked for changes.
         """
         from medharness.services.cr_generation import generate_code  # noqa: PLC0415
-        from medharness.workflows.cr_state import assert_cr_active  # noqa: PLC0415
+        from medharness.services.cr_state import assert_cr_active  # noqa: PLC0415
         dhf: Path = ctx.obj["dhf"]
         try:
             store = open_store(ctx.obj["dhf"])

medharness/cli/init.py

@@ -12,5 +12,5 @@ def init_cmd() -> None:
         Takes no prompts — the project name is derived from the directory name.
         Existing files are not overwritten.
         """
-        from medharness.workflows.init import run_init
+        from medharness.scaffold import run_init
         click.echo(json.dumps(run_init()))

medharness/workflows/init.py → medharness/scaffold.py

@@ -43,7 +43,7 @@
 # DHF scaffold
 # ---------------------------------------------------------------------------
 
-def _scaffold_dhf(project_dir: Path) -> None:
+def scaffold_dhf(project_dir: Path) -> None:
     """Create DHF structure inside project_dir from bundled templates."""
     project_dir.mkdir(parents=True, exist_ok=True)
 
@@ -93,7 +93,7 @@ def _substitutable_files(project_dir: Path):
             yield Path(dirpath) / filename
 
 
-def _replace_placeholders(project_dir: Path, project_name: str) -> None:
+def replace_placeholders(project_dir: Path, project_name: str) -> None:
     """Substitute template placeholders in scaffolded content."""
     try:
         medharness_version = pkg_version("medharness")
@@ -252,8 +252,8 @@ def say(text: str = "", **style) -> None:
 
     before = {f for f in project_dir.rglob("*") if f.is_file()}
     steps = [
-        ("Scaffold DHF structure", lambda: (_scaffold_dhf(project_dir),
-                                            _replace_placeholders(project_dir, project_name))),
+        ("Scaffold DHF structure", lambda: (scaffold_dhf(project_dir),
+                                            replace_placeholders(project_dir, project_name))),
         ("Write AGENTS.md and CLAUDE.md", lambda: _write_agent_files(project_dir, project_name)),
         ("Write .gitignore", lambda: _write_gitignore(project_dir)),
     ]

medharness/services/cr_generation.py

@@ -345,11 +345,11 @@ def generate_code(
         if code_review_verdict != "needs_revision" or review_cycle >= _MAX_CODE_REVIEW_CYCLES:
             break
 
+        issues = "\n".join(f"- {issue}" for issue in review_data["issues"])
         run.call(
             f"run_code_fix_{review_cycle}",
-            f"The code review for {cr_id} found issues. "
-            f"Fix each issue flagged in the review above — modify only the affected files. "
-            f"Do not make unrelated changes.",
+            f"The code review for {cr_id} found issues:\n{issues}\n\n"
+            f"Fix each one — modify only the affected files. Do not make unrelated changes.",
             develop_llm, critical=False,
         )
 

medharness/services/stage_run.py

@@ -241,9 +241,8 @@ def _augment_review_prompt(base: str, errors: list[dict]) -> str:
     if not errors:
         return base + (
             "\n\n## Deterministic Checks (already passed)\n\n"
-            "Schema, traceability, and the presence of all spec `affected_items` "
-            "(or required `@links:` test annotations) have been verified "
-            "mechanically. Do not re-derive them — focus on judgment questions "
+            "Schema, traceability, and the CR's recorded `affected_items` "
+            "have been verified mechanically. Do not re-derive them — focus on judgment questions "
             "that a script cannot answer."
         )
     residual = "\n".join(f"- {e.get('field', '?')}: {e.get('issue', '')}" for e in errors)

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "medharness"
-version = "0.54.0"
+version = "0.54.1"
 description = "Open-source design-controlled development infrastructure for medical device and SaMD teams — includes dhfkit"
 readme = "README.md"
 license = { text = "MIT" }