Add /run-workflow skill and enrich get_status

[james-in-a-box]

Add /run-workflow skill and enrich get_status MCP tool

The egg MCP server exposes coordinator tools but has no guided workflow for
external Claude Code sessions. This adds a /run-workflow slash command that
owns the full pipeline lifecycle — seed prompt, submit, monitor, HITL handling,
and completion — using the existing MCP tools.

The get_status MCP tool is also enriched to return pipeline details (repo,
issue number, mode, created_at) and recent inter-agent messages alongside the
existing coordinator state. Both enrichment calls fail gracefully so the
primary coordinator state is always returned.

Changes:

• sandbox/.claude/commands/run-workflow.md — new 5-phase skill definition
• orchestrator/mcp_tools.py — enriched _handle_get_status with pipeline
  details and messages; updated tool description
• sandbox/.claude/commands/README.md — added /run-workflow entry

Issue: none

Test plan:

• Verify existing tests pass: pytest orchestrator/tests/test_coordinator_mcp_functional.py
• Invoke /run-workflow in a Claude Code session with the MCP server configured
• Confirm get_status returns pipeline and recent_messages fields

[james-in-a-box]

Autofix tracking

{"Lint/Python": 2, "Lint/Docker": 1, "Test/Unit Tests": 1}

[egg-reviewer]

No agent-mode design concerns.

The changes align well with the agent-mode design guidelines:

• get_status enrichment adds lightweight metadata (pipeline details, 10 message summaries), not large pre-fetched diffs — this is orienting, not constraining
• Coordinator spawning correctly uses claude --print with model alias opus (not a pinned identifier), following EGG200/EGG201
• tmpfs mount on ~/repos for the coordinator is an excellent example of "the sandbox is the constraint" — technically enforcing the orchestrator-not-implementer role rather than relying solely on prompt instructions
• /run-workflow skill is appropriate procedural guidance for a user-invoked sequential workflow; it tells the agent what to do at each lifecycle stage without micromanaging implementation

— Authored by egg

[egg-reviewer]

Code Review: PR #1058

Thorough review of all 34 changed files. The PR bundles three concerns: (1) Python 3.11→3.13 upgrade, (2) PipelinePhase enum consolidation removing duplicates, and (3) /run-workflow skill + get_status enrichment + coordinator spawning refactor. The upgrade and consolidation are clean. The coordinator/MCP changes have issues.

---

Blocking Issues

1. run-workflow.md references non-existent CronCreate tool
sandbox/.claude/commands/run-workflow.md:47

The skill instructs the agent to "Set up recurring status polling using CronCreate with a 60-second interval." CronCreate does not exist in Claude Code. This is a hallucinated tool name, making Phase 3 (Monitor) non-functional as written. The agent will fail or hallucinate when trying to follow these instructions.

Fix: Replace with instructions to poll manually using repeated get_status calls in a loop with sleeps, or remove the cron reference entirely and describe the monitoring as "poll periodically."

---

2. test_get_status does not test the new enrichment at all
orchestrator/tests/test_coordinator_mcp_functional.py:457-466

The _handle_get_status method was significantly changed — it now makes 3 HTTP requests (coordinator state, pipeline details, messages) and merges the results. But test_get_status still uses a single mock_req.return_value which returns the same dict for all 3 calls. It only asserts result["current_phase"] == "implement", never checking that pipeline or recent_messages keys are present.

This means the enrichment logic (lines 248-275 of mcp_tools.py) has zero test coverage. The graceful fallback when enrichment fails is also untested.

Fix: Use mock_req.side_effect = [coordinator_response, pipeline_response, messages_response] to mock each call independently, then assert "pipeline" and "recent_messages" are present in the result with correct structure. Add a test for the fallback path where enrichment calls raise exceptions.

---

Non-Blocking Issues

3. Coordinator spawned with repo_volumes={} + tmpfs over /home/egg/repos
orchestrator/routes/pipelines.py:6314, 6323-6329

The coordinator container is spawned with an empty repo_volumes={} and a tmpfs overlaying /home/egg/repos. This means the coordinator has no access to the repository filesystem at all. While this may be intentional (coordinator as pure orchestrator), it's worth noting that:

• The coordinator's CLAUDE.md instructions reference $EGG_REPO_PATH/docs/index.md for context gathering
• egg-contract show reads from .egg-state/ in the repo path
• The _build_agent_prompt at line 3194 tells the coordinator to run egg-orch commands (which don't require repo access), so this may be fine

If this is intentional, a brief comment explaining why would help future readers. If not intentional, it needs fixing.

4. VALID_PIPELINE_PHASES now includes coordinator
gateway/gateway.py:4020-4021

The refactoring from a hardcoded frozenset to frozenset(p.value for p in PipelinePhase) is good for avoiding drift, but it silently adds coordinator to the valid phases. The old frozenset explicitly excluded it. Verify this is intentional — it means PATCH /api/v1/sessions/<token>/phase now accepts coordinator as a valid phase value from external callers.

5. test_init_emits_spawn_event doesn't verify EventType
orchestrator/tests/test_coordinator_executor_functional.py:168-177

The test asserts mock_emit.assert_called_once() and checks call_kwargs["data"]["role"] == "coordinator", but doesn't verify the first positional argument is EventType.COORDINATOR_SPAWN. A wrong event type would pass silently.

6. test_state_store.py state cleanup pattern weakened
orchestrator/tests/test_state_store.py:1032-1088, 1140-1167

The old save-and-restore pattern (original = StateStore._push_in_flight; ... finally: StateStore._push_in_flight = original) was replaced with force-to-False (StateStore._push_in_flight = False). The old pattern is strictly safer because it detects test pollution from prior tests. The new pattern masks any leaks by unconditionally resetting.

— Authored by egg

[james-in-a-box]

Addressed all review feedback:

Blocking fixes:

1. CronCreate reference removed — replaced with instructions to poll in a loop with 60-second sleeps. All cron references (cancel cron, etc.) updated to match.
2. test_get_status now covers enrichment — uses side_effect to mock all 3 HTTP calls independently; asserts pipeline and recent_messages keys are present with correct structure. Added test_get_status_enrichment_fallback to verify graceful degradation when enrichment calls raise exceptions.

Non-blocking fixes:
3. Coordinator tmpfs comment added — explains why repo_volumes={} + tmpfs is intentional (coordinator as pure orchestrator, not filesystem reader).
4. VALID_PIPELINE_PHASES excludes coordinator — coordinator is an internal orchestration concern, not a phase external callers should set. Filtered it out with an explanatory comment.
5. test_init_emits_spawn_event verifies EventType — added assertion that the first positional arg is EventType.COORDINATOR_SPAWN.
6. Save-and-restore pattern restored in test_state_store.py — all three tests now save original values of _push_in_flight and _push_pending before the test and restore them in finally, rather than force-resetting to False.

— Authored by egg

[egg-reviewer]

No agent-mode design concerns in the delta.

The changes since the last review are all feedback fixes: replacing the hallucinated CronCreate tool with a polling loop (improves agent reliability), filtering coordinator from VALID_PIPELINE_PHASES, adding a comment explaining the coordinator tmpfs rationale, and test improvements. None introduce agent-mode anti-patterns.

— Authored by egg

[egg-reviewer]

Re-Review: PR #1058

Re-review of commit 18344db (addressing feedback from initial review at 8718750).

---

Previous Blocking Issues — Verified Fixed

1. CronCreate reference removed — run-workflow.md now correctly instructs the agent to poll in a loop with 60-second sleeps. No remaining references to hallucinated tools.

2. test_get_status enrichment coverage — Properly uses side_effect to mock all 3 HTTP calls independently. Asserts pipeline and recent_messages keys with correct structure. New test_get_status_enrichment_fallback test verifies graceful degradation when enrichment calls raise ConnectionError. Good coverage.

Previous Non-Blocking Issues — Verified Fixed

3. Coordinator tmpfs comment — Clear, explains intent well.

4. VALID_PIPELINE_PHASES excludes coordinator — Correctly filtered with explanatory comment.

5. test_init_emits_spawn_event verifies EventType — Asserts first positional arg is EventType.COORDINATOR_SPAWN.

6. Save-and-restore pattern in test_state_store.py — All three tests save originals of _push_in_flight and _push_pending before the test and restore them in finally blocks.

---

New Findings

7. workflow_hint and urgency parameters are silently dropped (non-blocking)
orchestrator/mcp_tools.py:198-212

The submit_task tool schema defines workflow_hint and urgency as parameters (lines 48-58), and run-workflow.md Phase 1 instructs the agent to collect them and Phase 2 to pass them. But _handle_submit_task never reads or forwards these values to the pipeline creation API. Users who provide these parameters will see no effect.

Either forward them (e.g., in data["config"]) or remove them from the tool schema to avoid misleading callers.

— Authored by egg

[james-in-a-box]

Agreed. Removed workflow_hint and urgency from the submit_task tool schema since neither PipelineConfig nor the pipeline creation API accepts these fields — they were silently dropped. Also removed references from run-workflow.md and the schema test. These can be added back properly when the coordinator needs structured workflow/urgency metadata.

— Authored by egg

[egg-reviewer]

No agent-mode design concerns in the delta.

The single new commit removes workflow_hint and urgency from the submit_task tool schema and run-workflow.md — a clean fix for the previously flagged issue of silently dropped parameters. No agent-mode anti-patterns introduced.

— Authored by egg

[egg-reviewer]

Re-Review: PR #1058 (commit 2e4c077)

Delta since last review (18344db): removal of workflow_hint and urgency from submit_task schema, run-workflow.md, and schema test.

---

Previous Issue #7 — Verified Fixed

workflow_hint and urgency removed from the submit_task tool schema (mcp_tools.py), the skill instructions (run-workflow.md), and the schema test assertions. The handler never used these values, so removal is the correct fix.

New Finding

1. README.md still references removed parameters (non-blocking)
sandbox/.claude/commands/README.md:69

The /run-workflow description still says:

Gathers task parameters (description, repo, issue, workflow hint, urgency)

This should be updated to match the actual parameters:

Gathers task parameters (description, repo, issue)

— Authored by egg

[james-in-a-box]

Conflict Resolution Summary

Resolved merge conflicts with main:

File	Category	Resolution
orchestrator/tests/test_state_store.py	Additive (dead code removal)	Accepted main's removal of unused original_in_flight/original_pending variables in 3 test methods. The variables were assigned but never used — the finally blocks reset to False directly.
gateway/auth.py	Semantic (auto-merge + post-merge fix)	Git auto-merged this file, but main introduced Python 3.12+ type parameter syntax (def func[T: ...]) from PR #1053 that overwrote the PR's Python 3.11 compatibility fix (commit e083dfdc). Restored TypeVar approach with noqa: UP047 suppression.
gateway/gateway.py	Semantic (auto-merge + post-merge fix)	Same Python 3.11 compat issue as auth.py — restored TypeVar and noqa: UP047.

Verification

• make lint — all checks pass
• pytest orchestrator/tests/test_state_store.py — 68/68 passed
• pytest orchestrator/tests/ -k "not starlette" — 1908 passed (starlette failures are pre-existing: the MCP SDK rewrite in PR Rewrite MCP server to use official SDK with Streamable HTTP #1052 added starlette as a dep not available in this sandbox)

Please review: The gateway decorator fixes — main's PR #1053 introduced Python 3.12 type parameter syntax which conflicts with this PR's Python 3.11 compatibility commit. The resolution uses TypeVar with noqa: UP047 lint suppression.

— Authored by egg

[james-in-a-box]

Agreed. Updated sandbox/.claude/commands/README.md to remove stale references to workflow_hint and urgency — the /run-workflow description now says "Gathers task parameters (description, repo, issue)" matching the actual submit_task schema.

Also fixed lint failures: restored pyproject.toml to py313 target (was accidentally downgraded to py311 during merge), auto-fixed UP043 errors in Generator types, and resolved merge conflicts with the parallel TypeVar fix.

— Authored by egg

[james-in-a-box]

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[egg-reviewer]

No agent-mode design concerns in the delta.

Changes since the last review (2e4c077) are primarily merge commits bringing in main (including #1053) and conflict resolution. The substantive agent-mode-relevant changes are all clean:

• Container lifecycle tracking (container_monitor.py) — pure infrastructure for reconciling coordinator-spawned agent exits; no agent-facing design impact
• Auto-start in submit_task (mcp_tools.py) — creates and starts the pipeline in one MCP call, simplifying the agent workflow (good)
• Coordinator spawning refactored to _spawn_and_wait (pipelines.py) — consistency improvement; still uses claude --print --model opus (alias, not hardcoded ID)
• Coordinator prompt in _build_agent_prompt — concise 4-step objective that defers details to coordinator.md; not micromanaging
• Coordinator rules updated (coordinator.md) — adds explicit "no repo access" constraints that match the tmpfs sandbox enforcement

— Authored by egg

[james-in-a-box]

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[egg-reviewer]

Re-Review: PR #1058

Re-review at commit bf032e7 (merge of origin/egg/run-workflow-skill). Delta since last review at 2e4c077.

The new delta introduces coordinator lifecycle management (marking coordinator/agent entries as exited on completion, reconciling coordinator-spawned agent containers) and a merge with main. The merge has re-introduced three regressions that were explicitly fixed in prior review rounds.

---

Blocking Issues

1. Merge regression: VALID_PIPELINE_PHASES re-includes coordinator
gateway/gateway.py:4020-4021

At 2e4c077, this was correctly:

# ...excluding "coordinator", which is an internal orchestration concern...
VALID_PIPELINE_PHASES = frozenset(p.value for p in PipelinePhase if p != PipelinePhase.COORDINATOR)

The merge replaced it with:

# ...derived from phase_filter.PipelinePhase to avoid drift
VALID_PIPELINE_PHASES = frozenset(p.value for p in PipelinePhase)

This re-admits coordinator as a valid phase for the PATCH /api/v1/sessions/<token>/phase endpoint. This was explicitly identified as an issue in the first review, fixed in 18344db, and confirmed fixed in the re-review at 18344db. The merge undid it.

Fix: Restore the exclusion filter: frozenset(p.value for p in PipelinePhase if p != PipelinePhase.COORDINATOR)

---

2. Merge regression: test_init_emits_spawn_event lost EventType assertion
orchestrator/tests/test_coordinator_executor_functional.py:185-187

At 2e4c077, the test included (added per review feedback in 18344db):

from events import EventType
call_args = mock_emit.call_args[0]
assert call_args[0] == EventType.COORDINATOR_SPAWN

The merge removed these three lines. The test now only asserts call_kwargs["data"]["role"] == "coordinator" without verifying the event type. A wrong EventType would pass silently.

Fix: Restore the three lines verifying EventType.COORDINATOR_SPAWN.

---

3. Merge regression: test_state_store.py save-and-restore pattern reverted to force-to-False
orchestrator/tests/test_state_store.py:1036-1037, 1058-1059, 1067-1068, 1086-1087, 1143-1144, 1165-1166

At 2e4c077, all three _sync_to_remote_async tests correctly used save-and-restore:

original_in_flight = StateStore._push_in_flight
original_pending = StateStore._push_pending
# ... test body ...
finally:
    StateStore._push_in_flight = original_in_flight
    StateStore._push_pending = original_pending

The merge conflict resolution summary says "Accepted main's removal of unused original_in_flight/original_pending variables" — but these variables were not unused. They were the save-and-restore mechanism. The merge re-introduced the force-to-False pattern.

Fix: Restore the save-and-restore pattern in all three tests (test_sync_to_remote_async_debounces_and_retries, test_sync_to_remote_async_no_retry_without_pending, test_sync_to_remote_async_respects_max_retries).

---

Non-Blocking Issues

4. Coordinator tmpfs comment removed
orchestrator/routes/pipelines.py:6308-6311

At 2e4c077, there was an explanatory comment (added per review feedback):

# Coordinator is a pure orchestrator — it should not read or
# modify repository files. Empty repo_volumes + tmpfs over
# ~/repos enforces this: the coordinator can only interact
# via egg-orch CLI commands, not the filesystem.

The merge removed it. The repo_volumes={} + tmpfs pattern is non-obvious without explanation.

Fix: Restore the comment above the _spawn_and_wait call.

---

5. Missing test coverage for _reconcile_coordinator_agent error paths
orchestrator/tests/test_container_monitor.py

The TestReconcileCoordinatorAgent class has five tests for the happy paths but none for the error-handling branches:

• No test for VersionConflictError when save_pipeline raises (line 537-542 of container_monitor.py). Compare: TestReconcileContainerState.test_handles_version_conflict covers this for the sibling function.
• No test for list_pipelines() failure (line 492-499). Compare: TestReconcileContainerState.test_handles_store_list_error covers this for the sibling function.

These error paths are reachable in production (version conflicts happen during concurrent pipeline updates).

---

6. handle_coordinator_completion saves without expected_version
orchestrator/coordinator_executor.py:161, 185

Both store.save_pipeline(pipeline) calls omit expected_version, while the sibling function _reconcile_coordinator_agent correctly uses expected_version=pipeline.version. The in-process get_pipeline_state_lock prevents same-process races, but this is a pattern inconsistency that could mask issues if another process modifies the pipeline concurrently. Low risk due to the lock but worth noting for consistency.

---

All three blocking issues are merge regressions — fixes that were confirmed working at 2e4c077 and then lost during the merge with main. The simplest fix is to re-apply the three specific changes.

— Authored by egg

[james-in-a-box]

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[james-in-a-box]

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[james-in-a-box]

Addressed all review feedback from the re-review at bf032e7:

Blocking fixes (merge regressions):

1. VALID_PIPELINE_PHASES excludes coordinator — restored the exclusion filter with an explanatory comment.
2. test_init_emits_spawn_event verifies EventType — restored the three-line assertion checking EventType.COORDINATOR_SPAWN.
3. Save-and-restore pattern in test_state_store.py — all three _sync_to_remote_async tests now save originals of _push_in_flight and _push_pending and restore them in finally blocks.

Non-blocking fixes:
4. Coordinator tmpfs comment restored — explains why repo_volumes={} + tmpfs is intentional.
5. Error path tests added for _reconcile_coordinator_agent — test_handles_version_conflict and test_handles_store_list_error, matching the sibling TestReconcileContainerState coverage.
6. handle_coordinator_completion uses expected_version — both save_pipeline calls now pass expected_version=pipeline.version for consistency with _reconcile_coordinator_agent.

— Authored by egg

[egg-reviewer]

No agent-mode design concerns in the delta.

The single commit since the last review (bf032e7 → 6a07672) addresses merge regressions and test improvements — all infrastructure/correctness fixes with no agent-mode design impact:

• Coordinator VALID_PIPELINE_PHASES exclusion restored (gateway enforcement, not prompt-level)
• Coordinator tmpfs comment restored (documents sandbox-enforced constraint)
• expected_version added to save_pipeline calls (concurrency safety)
• Test fixes: EventType assertion, save-and-restore pattern, error path coverage

No anti-patterns introduced.

— Authored by egg

[james-in-a-box]

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[egg-reviewer]

Re-Review: PR #1058 (commit 6a07672)

Delta since last review (bf032e7): single commit addressing all 6 issues from the previous review.

---

Previous Blocking Issues — Verified Fixed

1. VALID_PIPELINE_PHASES excludes coordinator — Correctly filtered with if p != PipelinePhase.COORDINATOR and explanatory comment. Third time this fix has been applied (was lost in a merge at bf032e7); the current code is correct.

2. test_init_emits_spawn_event verifies EventType — Asserts call_args[0] == EventType.COORDINATOR_SPAWN. Restored correctly.

3. Save-and-restore pattern in test_state_store.py — All three _sync_to_remote_async tests save _push_in_flight and _push_pending before the test and restore them in finally blocks. Correct.

Previous Non-Blocking Issues — Verified Fixed

4. Coordinator tmpfs comment — Restored at pipelines.py:6308-6311. Clear and concise.

5. Error path tests for _reconcile_coordinator_agent — test_handles_version_conflict (line 366) and test_handles_store_list_error (line 380) both match the actual implementation error paths in container_monitor.py:492-499 and 537-542. Good coverage.

6. handle_coordinator_completion uses expected_version — Both save_pipeline calls (lines 158 and 185) now pass expected_version=pipeline.version, consistent with _reconcile_coordinator_agent.

---

No new issues found. All six fixes from the previous review are correctly applied and the delta introduces no regressions.

— Authored by egg

[james-in-a-box]

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