prizmkit 1.1.159 → 1.1.161

package/bundled/dev-pipeline/templates/sections/runtime-commit-handoff.md

@@ -5,31 +5,25 @@ The Python runtime, not the AI session, executes the pipeline's local Git commit
 After Code Review, all configured verification, `TEST_PASS`, family reports/summaries, and retrospective have completed:
 
 1. As the session orchestrator, validate every required stage artifact and result first. Atomic Skills do not perform this sequencing check.
-2. Invoke `/prizmkit-committer` with the same artifact root, exact readiness evidence, and request path:
+2. Re-inventory the complete final Git-visible workspace: staged, unstaged, added, deleted, renamed, copied, and non-ignored untracked content. Confirm Code Review and Test authority covers every behavior-affecting change, including correct work that predated this session or lives in framework, generated, instruction, lock, or host-support paths. If production behavior changed after those gates, re-enter them before commit preparation.
+3. Invoke `/prizmkit-committer` with the same artifact root, exact readiness evidence, and request path:
 
    ```text
-   /prizmkit-committer operation=prepare-runtime-commit artifact_dir={{ARTIFACT_DIR}} evidence_paths=<exact validated artifact paths> excluded_paths={{ARTIFACT_DIR}}/workflow-checkpoint.json request_path={{ARTIFACT_DIR}}/runtime-commit-request.json
+   /prizmkit-committer operation=prepare-runtime-commit artifact_dir={{ARTIFACT_DIR}} evidence_paths=<exact validated artifact paths> request_path={{ARTIFACT_DIR}}/runtime-commit-request.json
    ```
 
-3. The committer validates only the supplied evidence and final diff, then classifies paths before writing the request:
-   - all `.prizmkit/**` paths are PrizmKit-internal and stay outside the task commit, including config, plans, Prizm docs, lifecycle Artifacts, Runtime files, and state;
-   - `AGENTS.md`, `skills-lock.json`, installed platform directories, and local platform settings are support data and stay outside the task commit;
-   - project-specific transient data must already be covered by Git ignore rules;
-   - every other Git-visible path must be justified task output and included exactly, otherwise the handoff blocks.
-
-   It then rejects sensitive/unrelated/unknown paths, generates one Conventional Commit message, and writes this request without staging or committing:
+4. The committer validates the complete final workspace without a caller-supplied path manifest or provenance classification. Ignored paths remain local and never block or require force-add. Merge conflicts, Secrets, sensitive local content, known incorrect or incoherent changes, unverifiable content, and stale readiness evidence still block. It generates one truthful Conventional Commit message and writes this request without staging or committing:
 
    ```json
    {
-     "schema_version": 1,
+     "schema_version": 2,
      "artifact_dir": "{{ARTIFACT_DIR}}",
      "base_head": "<current HEAD commit hash>",
-     "commit_message": "<type>(<scope>): <description>",
-     "intended_paths": ["<exact project-relative changed path>"]
+     "commit_message": "<type>(<scope>): <description>"
    }
    ```
 
-4. Require the stage-local result `COMMIT_REQUEST_READY`. Then this injected session—not the Skill—marks `prizmkit-committer` `in_progress` with `stage_result=COMMIT_PENDING` through the checkpoint helper. Do not mark it completed or write `COMMITTED`.
-5. Stop normal work after the valid request and checkpoint handoff exist. Do not run `git add`, `git commit`, `git commit --amend`, merge, push, or create additional files.
+5. Require the stage-local result `COMMIT_REQUEST_READY`. Then this injected session—not the Skill—marks `prizmkit-committer` `in_progress` with `stage_result=COMMIT_PENDING` through the checkpoint helper. Do not mark it completed or write `COMMITTED`.
+6. Stop normal work after the valid request and checkpoint handoff exist. Do not run `git add`, `git commit`, `git commit --amend`, merge, push, or create additional task files.
 
-The runtime validates exact task-owned path coverage outside recognized internal/support namespaces, rejects a request that explicitly names one of those namespaces, stages only the requested literal paths, executes and verifies the local commit, finalizes the Runtime-owned checkpoint to `COMMITTED`, and then performs its configured merge/publication behavior. Unknown Git-visible paths are not silently ignored: they produce a mismatch and preserve the task checkout for recovery. A malformed, stale, unsafe, incomplete, or contradictory request also blocks without deleting user data.
+The Runtime validates the pathless schema, base, complete non-ignored workspace, sensitive path safeguards, merge state, and causal bookkeeping boundary. It stages the complete workspace, omitting only the exact active request/checkpoint whose final receipt cannot truthfully precede the commit; verifies a non-empty commit with the expected parent and message; records its Git receipt; and only then finalizes `COMMITTED` and performs configured integration. A malformed, stale, unsafe, incomplete, or contradictory handoff blocks without deleting user data.

package/bundled/dev-pipeline/tests/test_generate_bootstrap_prompt.py

@@ -1381,6 +1381,9 @@ class TestHeadlessPromptCleanupF033:
                 assert artifact in prompt
             assert "Atomic Skills write only their stage-owned artifacts and domain results" in prompt
             assert "COMMIT_REQUEST_READY" in prompt
+            assert '"schema_version": 2' in prompt
+            assert '"intended_paths"' not in prompt
+            assert "complete final Git-visible workspace" in prompt
             assert "workflow_state_path" not in prompt
             assert "outcome=RETRO_COMPLETE" in prompt
             assert "Never recreate the testing-local repair loop" in prompt
@@ -1554,11 +1557,12 @@ class TestFeatureBootstrapShellExtraction:
         assert "text search . --pattern \"123-prompt-cleanup\" --json" in tier3
         assert "text count .prizmkit/specs/123-prompt-cleanup/plan.md --pattern \"- [ ]\"" in tier3
         assert "/prizmkit-committer operation=prepare-runtime-commit" in tier3
-        assert "Require `COMMIT_REQUEST_READY`; this session records `COMMIT_PENDING`" in tier3
-        assert "The Python runtime validates the request" in tier3
-        assert "all `.prizmkit/**` paths are PrizmKit-internal" in tier3
-        assert "project-specific transient data must already be covered by git ignore rules" in tier3.lower()
-        assert "Unknown Git-visible paths are not silently ignored" in tier3
+        assert "Require a schema-v2 pathless request and `COMMIT_REQUEST_READY`" in tier3
+        assert "The Python runtime re-enumerates and commits the complete non-ignored workspace" in tier3
+        assert "validate the complete Git-visible workspace" in tier3
+        assert "Code Review and Test authority must cover every behavior-affecting visible change" in tier3
+        assert "Ignored paths remain naturally absent" in tier3
+        assert "Never force-add or change/interpret project ignore policy" in tier3
         assert "git add" not in tier3
         assert "git commit" not in tier3
 

package/bundled/dev-pipeline/tests/test_generate_bugfix_prompt.py

@@ -596,8 +596,10 @@ class TestBugfixCheckpointGeneration:
         assert "operation=prepare-runtime-commit" in prompt
         assert "NEVER ask for user confirmation" in prompt
         assert "The Python runtime, not the AI session, executes" in prompt
-        assert "all `.prizmkit/**` paths are PrizmKit-internal" in prompt
-        assert "Unknown Git-visible paths are not silently ignored" in prompt
+        assert "complete final Git-visible workspace" in prompt
+        assert '"schema_version": 2' in prompt
+        assert '"intended_paths"' not in prompt
+        assert "Ignored paths remain local" in prompt
         assert "push_authorized\": true" not in prompt
         assert ".prizmkit/bugfix/B-001/" in prompt
         assert "write the session status" not in prompt.lower()

package/bundled/dev-pipeline/tests/test_generate_refactor_prompt.py

@@ -435,8 +435,10 @@ class TestRefactorCheckpointGeneration:
         assert "local_commit_authorized" not in prompt
         assert "operation=prepare-runtime-commit" in prompt
         assert "The Python runtime, not the AI session, executes" in prompt
-        assert "all `.prizmkit/**` paths are PrizmKit-internal" in prompt
-        assert "Unknown Git-visible paths are not silently ignored" in prompt
+        assert "complete final Git-visible workspace" in prompt
+        assert '"schema_version": 2' in prompt
+        assert '"intended_paths"' not in prompt
+        assert "Ignored paths remain local" in prompt
         assert "automatic push" not in prompt.lower()
         assert "push_authorized\": true" not in prompt
         assert "write the session status" not in prompt.lower()

package/bundled/dev-pipeline/tests/test_runtime_commit.py

@@ -171,16 +171,15 @@ def _write_commit_ready_checkpoint(root: Path) -> tuple[Path, Path]:
     return artifact_dir, checkpoint_path
 
 
-def _write_request(root: Path, artifact_dir: Path, base_head: str, paths: list[str]) -> Path:
+def _write_request(root: Path, artifact_dir: Path, base_head: str) -> Path:
     request_path = artifact_dir / "runtime-commit-request.json"
     request_path.write_text(
         json.dumps(
             {
-                "schema_version": 1,
+                "schema_version": 2,
                 "artifact_dir": artifact_dir.relative_to(root).as_posix(),
                 "base_head": base_head,
                 "commit_message": "fix(runtime): finalize prepared task",
-                "intended_paths": paths,
             }
         ),
         encoding="utf-8",
@@ -188,7 +187,7 @@ def _write_request(root: Path, artifact_dir: Path, base_head: str, paths: list[s
     return request_path
 
 
-def test_runtime_commit_executes_exact_request_and_finalizes_only_checkpoint(tmp_path):
+def test_runtime_commit_executes_complete_workspace_and_finalizes_only_checkpoint(tmp_path):
     base_head = _init_repo(tmp_path)
     artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
     caller_state = tmp_path / ".prizmkit" / "state" / "workflows" / "caller.json"
@@ -196,7 +195,7 @@ def test_runtime_commit_executes_exact_request_and_finalizes_only_checkpoint(tmp
     caller_state.write_text('{"owner":"external-coordinator"}\n', encoding="utf-8")
     expected_caller_state = caller_state.read_bytes()
     (tmp_path / "tracked.txt").write_text("after\n", encoding="utf-8")
-    _write_request(tmp_path, artifact_dir, base_head, ["tracked.txt"])
+    _write_request(tmp_path, artifact_dir, base_head)
 
     result = finalize_runtime_commit(
         tmp_path,
@@ -229,18 +228,18 @@ def test_runtime_commit_executes_exact_request_and_finalizes_only_checkpoint(tmp
         ".prizmkit/prizm-docs/src/counter.prizm",
     ],
 )
-def test_runtime_commit_excludes_tracked_prizmkit_internal_paths(tmp_path, durable_path):
+def test_runtime_commit_includes_tracked_prizmkit_path_from_workspace(tmp_path, durable_path):
     _init_repo(tmp_path)
     durable = tmp_path / durable_path
     durable.parent.mkdir(parents=True, exist_ok=True)
     durable.write_text("before\n", encoding="utf-8")
     _git(tmp_path, "add", "-f", durable_path)
-    _git(tmp_path, "commit", "-m", "track durable PrizmKit project data")
+    _git(tmp_path, "commit", "-m", "track project-selected PrizmKit data")
     base_head = _git(tmp_path, "rev-parse", "HEAD")
     artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
     (tmp_path / "tracked.txt").write_text("after\n", encoding="utf-8")
     durable.write_text("after\n", encoding="utf-8")
-    _write_request(tmp_path, artifact_dir, base_head, ["tracked.txt"])
+    _write_request(tmp_path, artifact_dir, base_head)
 
     result = finalize_runtime_commit(
         tmp_path,
@@ -249,24 +248,19 @@ def test_runtime_commit_excludes_tracked_prizmkit_internal_paths(tmp_path, durab
     )
 
     assert result.status == "committed", result
-    assert _git(
+    changed = set(_git(
         tmp_path,
         "diff-tree",
         "--no-commit-id",
         "--name-only",
         "-r",
         "HEAD",
-    ) == "tracked.txt"
+    ).splitlines())
+    assert changed == {"tracked.txt", durable_path}
     assert durable.read_text(encoding="utf-8") == "after\n"
-    assert durable_path in _git(
-        tmp_path,
-        "status",
-        "--short",
-        "--untracked-files=all",
-    )
 
 
-def test_runtime_commit_ignores_runner_support_paths_but_leaves_them_unmodified(tmp_path):
+def test_runtime_commit_includes_valid_host_support_paths_from_workspace(tmp_path):
     base_head = _init_repo(tmp_path)
     artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
     (tmp_path / "tracked.txt").write_text("after\n", encoding="utf-8")
@@ -274,7 +268,7 @@ def test_runtime_commit_ignores_runner_support_paths_but_leaves_them_unmodified(
     codex_config = tmp_path / ".codex" / "config.toml"
     codex_config.parent.mkdir()
     codex_config.write_text("[project]\ntrusted = true\n", encoding="utf-8")
-    _write_request(tmp_path, artifact_dir, base_head, ["tracked.txt"])
+    _write_request(tmp_path, artifact_dir, base_head)
 
     result = finalize_runtime_commit(
         tmp_path,
@@ -283,11 +277,11 @@ def test_runtime_commit_ignores_runner_support_paths_but_leaves_them_unmodified(
     )
 
     assert result.status == "committed"
-    assert _git(tmp_path, "diff-tree", "--no-commit-id", "--name-only", "-r", "HEAD") == "tracked.txt"
-    assert (tmp_path / "AGENTS.md").read_text(encoding="utf-8") == "@./AGENTS.private.md\n"
-    assert codex_config.read_text(encoding="utf-8") == "[project]\ntrusted = true\n"
-    untracked = set(_git(tmp_path, "ls-files", "--others", "--exclude-standard").splitlines())
-    assert {"AGENTS.md", ".codex/config.toml"}.issubset(untracked)
+    changed = set(
+        _git(tmp_path, "diff-tree", "--no-commit-id", "--name-only", "-r", "HEAD").splitlines()
+    )
+    assert changed == {"tracked.txt", "AGENTS.md", ".codex/config.toml"}
+    assert _git(tmp_path, "status", "--porcelain") == ""
 
 
 def test_runtime_commit_allows_task_path_adjacent_to_internal_namespace(tmp_path):
@@ -296,7 +290,7 @@ def test_runtime_commit_allows_task_path_adjacent_to_internal_namespace(tmp_path
     adjacent_path = tmp_path / ".prizmkitx" / "task.txt"
     adjacent_path.parent.mkdir()
     adjacent_path.write_text("task-owned\n", encoding="utf-8")
-    _write_request(tmp_path, artifact_dir, base_head, [".prizmkitx/task.txt"])
+    _write_request(tmp_path, artifact_dir, base_head)
 
     result = finalize_runtime_commit(
         tmp_path,
@@ -320,7 +314,7 @@ def test_runtime_commit_ignores_project_gitignored_transient_data(tmp_path):
     transient = tmp_path / "tmp" / "tool-cache.json"
     transient.parent.mkdir()
     transient.write_text('{"cache":true}\n', encoding="utf-8")
-    _write_request(tmp_path, artifact_dir, base_head, ["tracked.txt"])
+    _write_request(tmp_path, artifact_dir, base_head)
 
     result = finalize_runtime_commit(
         tmp_path,
@@ -333,12 +327,12 @@ def test_runtime_commit_ignores_project_gitignored_transient_data(tmp_path):
     assert transient.read_text(encoding="utf-8") == '{"cache":true}\n'
 
 
-def test_runtime_commit_rejects_unlisted_git_visible_change(tmp_path):
+def test_runtime_commit_includes_preexisting_git_visible_change_without_manifest(tmp_path):
     base_head = _init_repo(tmp_path)
     artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
     (tmp_path / "tracked.txt").write_text("after\n", encoding="utf-8")
-    (tmp_path / "unexpected.txt").write_text("unexpected\n", encoding="utf-8")
-    _write_request(tmp_path, artifact_dir, base_head, ["tracked.txt"])
+    (tmp_path / "preexisting.txt").write_text("validated existing work\n", encoding="utf-8")
+    _write_request(tmp_path, artifact_dir, base_head)
 
     result = finalize_runtime_commit(
         tmp_path,
@@ -346,16 +340,18 @@ def test_runtime_commit_rejects_unlisted_git_visible_change(tmp_path):
         checkpoint_path=checkpoint_path,
     )
 
-    assert result.status == "failed"
-    assert result.reason == "intended_paths_mismatch"
-    assert _git(tmp_path, "rev-parse", "HEAD") == base_head
+    assert result.status == "committed"
+    changed = set(
+        _git(tmp_path, "diff-tree", "--no-commit-id", "--name-only", "-r", "HEAD").splitlines()
+    )
+    assert changed == {"tracked.txt", "preexisting.txt"}
 
 
 def test_runtime_commit_recovers_commit_created_before_state_finalization(tmp_path):
     base_head = _init_repo(tmp_path)
     artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
     (tmp_path / "tracked.txt").write_text("after\n", encoding="utf-8")
-    _write_request(tmp_path, artifact_dir, base_head, ["tracked.txt"])
+    _write_request(tmp_path, artifact_dir, base_head)
     _git(tmp_path, "add", "tracked.txt")
     _git(tmp_path, "commit", "-m", "fix(runtime): finalize prepared task")
     committed_head = _git(tmp_path, "rev-parse", "HEAD")
@@ -372,15 +368,38 @@ def test_runtime_commit_recovers_commit_created_before_state_finalization(tmp_pa
     assert _git(tmp_path, "rev-list", "--count", f"{base_head}..HEAD") == "1"
 
 
+def test_runtime_commit_rejects_recovery_commit_containing_causal_bookkeeping(tmp_path):
+    base_head = _init_repo(tmp_path)
+    artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
+    (tmp_path / "tracked.txt").write_text("after\n", encoding="utf-8")
+    request_path = _write_request(tmp_path, artifact_dir, base_head)
+    _git(
+        tmp_path,
+        "add",
+        "-f",
+        "tracked.txt",
+        checkpoint_path.relative_to(tmp_path).as_posix(),
+        request_path.relative_to(tmp_path).as_posix(),
+    )
+    _git(tmp_path, "commit", "-m", "fix(runtime): finalize prepared task")
+
+    result = finalize_runtime_commit(
+        tmp_path,
+        artifact_dir=artifact_dir,
+        checkpoint_path=checkpoint_path,
+    )
+
+    assert result.status == "failed"
+    assert result.reason == "base_head_mismatch"
+
+
 def test_runtime_commit_recovers_after_checkpoint_finalization_failure(tmp_path, monkeypatch):
     import prizmkit_runtime.runtime_commit as runtime_commit
 
     base_head = _init_repo(tmp_path)
     artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
     (tmp_path / "tracked.txt").write_text("after\n", encoding="utf-8")
-    request_path = _write_request(
-        tmp_path, artifact_dir, base_head, ["tracked.txt"]
-    )
+    request_path = _write_request(tmp_path, artifact_dir, base_head)
 
     original_finalize = runtime_commit._finalize_checkpoint
     monkeypatch.setattr(
@@ -417,9 +436,7 @@ def test_runtime_commit_recovers_cleanup_after_completed_checkpoint(tmp_path, mo
     base_head = _init_repo(tmp_path)
     artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
     (tmp_path / "tracked.txt").write_text("after\n", encoding="utf-8")
-    request_path = _write_request(
-        tmp_path, artifact_dir, base_head, ["tracked.txt"]
-    )
+    request_path = _write_request(tmp_path, artifact_dir, base_head)
 
     original_unlink = Path.unlink
 
@@ -462,7 +479,7 @@ def test_runtime_commit_disables_repository_hooks(tmp_path):
     )
     hook.chmod(0o755)
     (tmp_path / "tracked.txt").write_text("after\n", encoding="utf-8")
-    _write_request(tmp_path, artifact_dir, base_head, ["tracked.txt"])
+    _write_request(tmp_path, artifact_dir, base_head)
 
     result = finalize_runtime_commit(
         tmp_path,
@@ -484,12 +501,7 @@ def test_runtime_commit_handles_rename_as_exact_delete_and_add(tmp_path):
     base_head = _git(tmp_path, "rev-parse", "HEAD")
     artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
     old_path.rename(tmp_path / "new-name.txt")
-    _write_request(
-        tmp_path,
-        artifact_dir,
-        base_head,
-        ["old-name.txt", "new-name.txt"],
-    )
+    _write_request(tmp_path, artifact_dir, base_head)
 
     result = finalize_runtime_commit(
         tmp_path,
@@ -513,28 +525,95 @@ def test_runtime_commit_handles_rename_as_exact_delete_and_add(tmp_path):
 @pytest.mark.parametrize(
     "unsafe_path",
     [
-        "../escape.txt",
-        ".git/config",
         ".env",
-        "AGENTS.md",
-        "skills-lock.json",
-        ".codex/config.toml",
-        ".CLAUDE/settings.local.json",
-        ".prizmkit/config.json",
-        ".prizmkit/prizm-docs/src/counter.prizm",
-        ".prizmkit/state/runtime.json",
-        ".prizmkit/dev-pipeline/cli.py",
-        ".prizmkit/scripts/helper.py",
-        ".prizmkit/manifest.json",
-        ".prizmkit/specs/001-runtime-commit/workflow-checkpoint.json",
-        ".prizmkit/specs/001-runtime-commit/runtime-commit-request.json",
+        "credentials.json",
+        "secrets.json",
+        "private.pem",
+        ".codex/settings.local.json",
     ],
 )
-def test_runtime_commit_rejects_unsafe_intended_paths(tmp_path, unsafe_path):
+def test_runtime_commit_rejects_sensitive_git_visible_workspace_path(tmp_path, unsafe_path):
+    base_head = _init_repo(tmp_path)
+    artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
+    unsafe = tmp_path / unsafe_path
+    unsafe.parent.mkdir(parents=True, exist_ok=True)
+    unsafe.write_text("sensitive\n", encoding="utf-8")
+    _write_request(tmp_path, artifact_dir, base_head)
+
+    result = finalize_runtime_commit(
+        tmp_path,
+        artifact_dir=artifact_dir,
+        checkpoint_path=checkpoint_path,
+    )
+
+    assert result.status == "failed"
+    assert result.reason == "sensitive_workspace_path"
+    assert _git(tmp_path, "rev-parse", "HEAD") == base_head
+
+
+def test_runtime_commit_rejects_empty_workspace(tmp_path):
+    base_head = _init_repo(tmp_path)
+    artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
+    _write_request(tmp_path, artifact_dir, base_head)
+
+    result = finalize_runtime_commit(
+        tmp_path,
+        artifact_dir=artifact_dir,
+        checkpoint_path=checkpoint_path,
+    )
+
+    assert result.status == "failed"
+    assert result.reason == "empty_workspace_change"
+    assert _git(tmp_path, "rev-parse", "HEAD") == base_head
+
+
+def test_runtime_commit_rejects_unresolved_merge_state(tmp_path):
+    _init_repo(tmp_path)
+    initial_branch = _git(tmp_path, "branch", "--show-current")
+    _git(tmp_path, "checkout", "-b", "other")
+    (tmp_path / "tracked.txt").write_text("other\n", encoding="utf-8")
+    _git(tmp_path, "add", "tracked.txt")
+    _git(tmp_path, "commit", "-m", "other change")
+    _git(tmp_path, "checkout", initial_branch)
+    (tmp_path / "tracked.txt").write_text("master\n", encoding="utf-8")
+    _git(tmp_path, "add", "tracked.txt")
+    _git(tmp_path, "commit", "-m", "master change")
+    base_head = _git(tmp_path, "rev-parse", "HEAD")
+    merged = subprocess.run(
+        ["git", "merge", "other"],
+        cwd=tmp_path,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.PIPE,
+        text=True,
+        check=False,
+    )
+    assert merged.returncode != 0
+    artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
+    _write_request(tmp_path, artifact_dir, base_head)
+
+    result = finalize_runtime_commit(
+        tmp_path,
+        artifact_dir=artifact_dir,
+        checkpoint_path=checkpoint_path,
+    )
+
+    assert result.status == "failed"
+    assert result.reason == "unresolved_merge_state"
+    assert _git(tmp_path, "rev-parse", "HEAD") == base_head
+
+
+def test_runtime_commit_rejects_already_staged_runtime_bookkeeping(tmp_path):
     base_head = _init_repo(tmp_path)
     artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
     (tmp_path / "tracked.txt").write_text("after\n", encoding="utf-8")
-    _write_request(tmp_path, artifact_dir, base_head, [unsafe_path])
+    request_path = _write_request(tmp_path, artifact_dir, base_head)
+    _git(
+        tmp_path,
+        "add",
+        "-f",
+        checkpoint_path.relative_to(tmp_path).as_posix(),
+        request_path.relative_to(tmp_path).as_posix(),
+    )
 
     result = finalize_runtime_commit(
         tmp_path,
@@ -543,17 +622,99 @@ def test_runtime_commit_rejects_unsafe_intended_paths(tmp_path, unsafe_path):
     )
 
     assert result.status == "failed"
-    assert result.reason == "commit_request_path_unsafe"
+    assert result.reason == "runtime_bookkeeping_staged"
     assert _git(tmp_path, "rev-parse", "HEAD") == base_head
 
 
-def test_runtime_commit_rejects_caller_orchestration_fields(tmp_path):
+def test_runtime_commit_rejects_schema_v1_path_manifest(tmp_path):
     base_head = _init_repo(tmp_path)
     artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
     (tmp_path / "tracked.txt").write_text("after\n", encoding="utf-8")
-    request_path = _write_request(
-        tmp_path, artifact_dir, base_head, ["tracked.txt"]
+    request_path = _write_request(tmp_path, artifact_dir, base_head)
+    request = json.loads(request_path.read_text(encoding="utf-8"))
+    request["schema_version"] = 1
+    request["intended_paths"] = ["tracked.txt"]
+    request_path.write_text(json.dumps(request), encoding="utf-8")
+
+    result = finalize_runtime_commit(
+        tmp_path,
+        artifact_dir=artifact_dir,
+        checkpoint_path=checkpoint_path,
+    )
+
+    assert result.status == "failed"
+    assert result.reason == "commit_request_invalid_schema"
+    assert _git(tmp_path, "rev-parse", "HEAD") == base_head
+
+
+def test_runtime_commit_includes_already_staged_and_unstaged_workspace(tmp_path):
+    _init_repo(tmp_path)
+    support = tmp_path / "AGENTS.md"
+    support.write_text("before\n", encoding="utf-8")
+    _git(tmp_path, "add", "AGENTS.md")
+    _git(tmp_path, "commit", "-m", "track support")
+    base_head = _git(tmp_path, "rev-parse", "HEAD")
+    artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
+    (tmp_path / "tracked.txt").write_text("after\n", encoding="utf-8")
+    support.write_text("after\n", encoding="utf-8")
+    _git(tmp_path, "add", "AGENTS.md")
+    _write_request(tmp_path, artifact_dir, base_head)
+
+    result = finalize_runtime_commit(
+        tmp_path,
+        artifact_dir=artifact_dir,
+        checkpoint_path=checkpoint_path,
     )
+
+    assert result.status == "committed"
+    changed = set(
+        _git(tmp_path, "diff-tree", "--no-commit-id", "--name-only", "-r", "HEAD").splitlines()
+    )
+    assert changed == {"AGENTS.md", "tracked.txt"}
+
+
+def test_runtime_commit_keeps_tracked_post_commit_bookkeeping_out_of_snapshot(tmp_path):
+    from prizmkit_runtime.gitops import HIDDEN_TOOL_WORKTREE_EXCLUDES
+
+    initial_head = _init_repo(tmp_path)
+    artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
+    request_path = _write_request(tmp_path, artifact_dir, initial_head)
+    checkpoint_rel = checkpoint_path.relative_to(tmp_path).as_posix()
+    request_rel = request_path.relative_to(tmp_path).as_posix()
+    _git(tmp_path, "add", "-f", checkpoint_rel, request_rel)
+    _git(tmp_path, "commit", "-m", "track runtime bookkeeping by project policy")
+    base_head = _git(tmp_path, "rev-parse", "HEAD")
+    _write_request(tmp_path, artifact_dir, base_head)
+    (tmp_path / "tracked.txt").write_text("after\n", encoding="utf-8")
+
+    result = finalize_runtime_commit(
+        tmp_path,
+        artifact_dir=artifact_dir,
+        checkpoint_path=checkpoint_path,
+    )
+
+    assert result.status == "committed", result
+    assert _git(tmp_path, "diff-tree", "--no-commit-id", "--name-only", "-r", "HEAD") == "tracked.txt"
+    assert checkpoint_rel not in _git(tmp_path, "diff-tree", "--no-commit-id", "--name-only", "-r", "HEAD")
+    visible = _git(
+        tmp_path,
+        "status",
+        "--porcelain",
+        "--",
+        ".",
+        *HIDDEN_TOOL_WORKTREE_EXCLUDES,
+    )
+    assert visible == ""
+    raw_status = _git(tmp_path, "status", "--porcelain", "--", checkpoint_rel, request_rel)
+    assert checkpoint_rel in raw_status
+    assert request_rel in raw_status
+
+
+def test_runtime_commit_rejects_caller_orchestration_fields(tmp_path):
+    base_head = _init_repo(tmp_path)
+    artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
+    (tmp_path / "tracked.txt").write_text("after\n", encoding="utf-8")
+    request_path = _write_request(tmp_path, artifact_dir, base_head)
     request = json.loads(request_path.read_text(encoding="utf-8"))
     request["caller_state_path"] = ".runtime/caller-state.json"
     request_path.write_text(json.dumps(request), encoding="utf-8")
@@ -573,9 +734,7 @@ def test_runtime_commit_rejects_ai_supplied_premature_runtime_hash(tmp_path):
     base_head = _init_repo(tmp_path)
     artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
     (tmp_path / "tracked.txt").write_text("after\n", encoding="utf-8")
-    request_path = _write_request(
-        tmp_path, artifact_dir, base_head, ["tracked.txt"]
-    )
+    request_path = _write_request(tmp_path, artifact_dir, base_head)
     request = json.loads(request_path.read_text(encoding="utf-8"))
     request["runtime_commit_hash"] = "a" * 40
     request_path.write_text(json.dumps(request), encoding="utf-8")
@@ -595,7 +754,7 @@ def test_runtime_commit_rejects_stale_base_head(tmp_path):
     base_head = _init_repo(tmp_path)
     artifact_dir, checkpoint_path = _write_commit_ready_checkpoint(tmp_path)
     (tmp_path / "tracked.txt").write_text("after\n", encoding="utf-8")
-    _write_request(tmp_path, artifact_dir, "a" * 40, ["tracked.txt"])
+    _write_request(tmp_path, artifact_dir, "a" * 40)
 
     result = finalize_runtime_commit(
         tmp_path,