Add SDLC pipeline support for Jira epics (#1557)

[james-in-a-box]

Context

Today submit_task <TICKET> runs the egg refine → plan pipeline
against a Jira ticket and produces one PR per ticket. A Jira
epic is a different shape of work: a multi-ticket container
that should fan out into N child tickets, each becoming its own
downstream implement pipeline. This PR teaches the orchestrator
to recognise epics, run the same refine → plan agents against
them with mode-aware prompts, and apply the resulting Jira
mutations (epic Description write, child create / edit /
Won't-Do, issue links) on HITL approval. It also adds the
reassess path so an epic that already has children classifies
them (Done / In-flight / Updatable) instead of re-creating
equivalent work.

Changes

1. Epic detection at submit_task time — pre-fetch the
   ticket's issuetype via the gateway, persist is_epic and
   pipeline_mode on the Pipeline model, and inject
   EGG_PIPELINE_MODE / EGG_IS_EPIC into the sandbox so the
   refiner / task-planner prompts know which mode to use. New
   mode arg on submit_task ('auto' / 'fresh' / 'reassess')
   lets the operator override the detector.
2. Mode-parameterised refiner / task-planner prompts — both
   prompts get a mode block so the same file covers ticket,
   github_issue, epic-fresh, and epic-reassess shapes. Epic
   prompts produce ticket-shaped task descriptions
   (Problem / Scope / Acceptance / OOS / Links) ready for direct
   paste into a Jira body.
3. Per-task Jira mapping on the contract — Task gets
   optional jira_key and jira_action
   ('create' / 'edit' / 'wontdo' / 'split-of' / 'consolidate-into')
   fields; the plan parser extracts them from the YAML appendix.
   The applier walks this mapping to drive idempotent re-runs.
4. New APPLIER agent role + apply phase + REVIEWER_CONTRACT
   apply-phase reviewer — PipelinePhase.APPLY joins the
   enum; VALID_TRANSITIONS gains PLAN -> APPLY and
   APPLY -> IMPLEMENT gated on Pipeline.is_epic. The
   orchestrator schedules an apply phase after every
   epic-mode HITL approval (refine and plan). The applier
   reads the contract + drafts and calls the existing jira
   sandbox CLI for create / edit / link mutations;
   REVIEWER_CONTRACT ACKs on contract-state convergence
   (every jira_action='create' Task has a jira_key,
   every Task's jira_action_status reached
   'applied' or 'failed', no in-flight child mutated
   without in-flight-confirmed). Task gains a
   jira_action_status lifecycle field so the applier can
   record per-call progress and idempotently recover from
   partial-apply failures.
5. Reassess sweep — orchestrator helper queries existing
   children (project = <P> AND parent = <K>) via the gateway
   JQL search; classifies each via statusCategory.key; feeds
   Updatable + In-flight + net-new context into the planner
   prompt; excludes Done children entirely (decision-5).
6. In-flight detection — orchestrator reverse-index
   jira_ticket → [pipelines] (with Pipeline.pr_url
   persisted on PR-open) plus a new read-only gateway route
   POST /api/v1/jira/ticket/remotelinks so human-opened PRs
   still get caught.
7. Won't-Do transitions — new gateway route POST /api/v1/jira/ticket/transition, orchestrator-only
   (loopback + shared-secret token), allowlisted to
   Won't Do / Won't Fix. Agent-facing Jira routes still
   deny transitions; the orchestrator-only route preserves the
   "creds only in gateway" invariant.
8. Tests — unit + integration coverage for every new path
   (model serialisation, plan-parser extraction, role registry,
   gateway route allowlists, applier mutation flow,
   in-flight classifier, reassess JQL, idempotency).

Impact

• Operators get a one-call submit_task jira_ticket="<EPIC>"
  surface for both fresh and reassessed epics. The host Claude
  session walks the same draft + decision HITL surface used
  today for tickets — no new UI.
• The egg pipeline can now mutate Jira state (Description writes,
  child tickets, links, Won't-Do transitions) on HITL approval.
  All mutations stay behind the gateway audit + idempotency
  cache; the only orchestrator-side credential addition is the
  new shared-secret loopback token for the transition route.
• Implement-phase pipelines for individual child tickets
  continue to work unchanged — each child runs submit_task <CHILD-KEY> exactly as today, with Independent implement phases #2137's slice-DAG
  stacking applying inside each child as needed.

Test Plan

Automated:

• make test covers unit suites for the new Pipeline / Task
  fields, plan-parser extraction of jira_key / jira_action,
  APPLIER role registration, in-flight classifier, reassess JQL
  shape, gateway /transition allowlist, gateway /remotelinks
  read, and applier mutation idempotency.
• make test-integration (kubectl-gated) exercises the
  end-to-end submit_task flow against a scripted-Jira fake
  under integration_tests/. Cover both fresh and reassess
  paths; assert epic Description write, child create + link,
  Won't-Do batch transition, and in-flight refusal.

Manual:

• From the host Claude session, run submit_task jira_ticket="<EPIC-KEY>" mode="auto" against a low-risk seed
  epic in a test Atlassian project. Walk the refine HITL gate;
  confirm the applier writes the analysis to the epic
  Description (visible in the Jira UI). Walk the plan HITL
  gate; confirm the applier creates child tickets, links them
  with Blocks / Relates, and (if any obsolete children
  present) transitions them to Won't Do with a comment
  pointing at the survivor.
• Re-run submit_task jira_ticket="<EPIC-KEY>-v2" mode="auto"
  after seeding a Done child + an In-flight child + an
  Updatable child + an obsolete child; confirm classification
  diff in the plan draft, confirm Done child is omitted from
  the plan, confirm in-flight child is not mutated without an
  explicit per-ticket HITL.
• Verify submit_task <CHILD-KEY> against any created child
  still works — the implement phase of a child pipeline is
  unchanged.

Manual Steps

Pre-merge:

• Update config/context-filters.yaml jira.projects to list
  the Atlassian project keys the epic pipeline may write to.
• Set jira.epic_link_field per project for any classic /
  team-managed project where the default parent is wrong
  (classic projects need customfield_10014).
• Add the orchestrator-only shared-secret token for the
  /transition route to the gateway secret bundle (rotate the
  existing Atlassian secret bundle).
• The orchestrator and gateway must be redeployed together;
  stage the rollout so both new routes (/transition +
  /remotelinks) land in lockstep.

Post-merge:

• Run a smoke test: submit_task jira_ticket="<TEST-EPIC>" mode="auto" against a seeded test epic in the test
  Atlassian project. Confirm the refine + plan HITL gates and
  the applier outcomes.
• Watch the gateway audit log for the first production
  /transition invocations to confirm the loopback +
  shared-secret check denies non-orchestrator callers.

Pipeline Context

Pipeline: issue-1557-v2
Issue: #1557

Per-phase BRC transcripts: refine, plan, implement-slice-1, implement-slice-2, implement-unattributed.

Authored-by: egg

[egg-reviewer]

Re-reviewed the delta 6a62df93..ea6adc08 (one new commit: "Address review feedback on PR #2678"). The agent-mode-relevant changes all move in the right direction and introduce no new anti-patterns.

Prompt-surface cleanups — the four agent prompt files (applier.md, refiner.md, reviewer-contract-apply.md, task-planner.md) drop the stale "not yet landed" / "zero callers" caveats now that the apply-phase drain hook and prep_mode_aware_prompt strip helper are wired. The reviewer prompt's handoff filename (wontdo.json) and accepted JSON shape (bare list or entries: [...] wrapper) now match what applier.md writes and what load_wontdo_handoff parses, closing the deadlock I flagged in my original CHANGES_REQUESTED review.

Auto-projection of the structured Task.notes prefix onto typed Task.jira_action_status / Task.jira_key (sandbox/egg_agent_tools/handlers/task.py::_project_notes_prefix) is a clean improvement on the interim TD shape — producers and consumers now see one coherent surface instead of two views that can drift. The prompt update in applier.md correctly directs reviewers to read the typed fields. Still acknowledged as a stopgap pending a typed mcp__task__set_status MCP.

Won't-Do drain idempotency gate (_entry_already_applied predicate passed from pipelines.py into run_wontdo_drain) keeps lifecycle ownership orchestrator-side — the agent writes one handoff file, the orchestrator decides whether to skip on re-runs. Right placement for state-machine logic.

Won't-Do /transition route documentation honestly notes that the launcher-secret bearer is mounted in sandbox containers too, so it is not a sandbox/orchestrator discriminator on its own; NetworkPolicy is the actual scoping mechanism. Clearer trust-model framing than before.

No direct LLM API calls, no hardcoded model IDs, no excessive pre-fetching, no human-consumer JSON requirements introduced.

— Authored by egg

[james-in-a-box]

Contract verification re-review: ea6adc0 (delta from 6a62df9)

Verdict: All review feedback addressed cleanly; no contract violations introduced. Previously verified criteria still hold.

Delta scope

One PR-authored commit since last review: ea6adc0 Address review feedback on PR #2678 — a focused feedback-addressing commit touching 16 files (493 / 78 lines).

Changes verified

Code:

• orchestrator/wontdo_drain.py:117-124,186-258 — Added is_already_applied predicate parameter to run_wontdo_drain. Skipped entries land in DrainResult.skipped and the on_entry_result callback is intentionally not invoked for them. Defensive: predicate exceptions are logged and treated as "not applied." Tightened except clauses (broad Exception removed; HTTPError.read catch narrowed to (OSError, UnicodeDecodeError)). The bare-comma form is valid under PEP 758 (project requires Python >=3.14).
• orchestrator/routes/pipelines.py:18608-18658 — _entry_already_applied closure loads the contract and matches entries by task_id first, falling back to jira_key; wired into run_wontdo_drain call. Acceptable idempotency design.
• orchestrator/routes/pipelines.py:1990-2010 — epic_mode='fresh' against a non-epic now returns HTTP 400 (reason='fresh_not_epic'), symmetric with the existing reassess rejection. mode='auto' still demotes silently, matching the comment's intent.
• orchestrator/jira_reassess.py — Dropped description from _REASSESS_FIELDS (planner re-authors per-task bodies; Atlassian's ADF dict was being silently dropped). Added jql_search_truncated warning when total > len(issues). ReassessChild.description field retained for backwards-compat JSON load — good.
• orchestrator/jira_epic.py:251 — Dropped redundant bool() wrap; the trailing if has_children already coerces.
• gateway/gateway.py:5309-5328,5520-5548 — Comment corrections only: clarifies that sandbox pods also mount the launcher secret, so the bearer is a coarse credential (NetworkPolicy + loopback scope are the actual orchestrator-vs-sandbox discriminator). No behavioral change.
• sandbox/egg_agent_tools/handlers/task.py:18-58,287-316 — Added _project_notes_prefix (parses jira_action_status=<val> / jira_key=<KEY> from first 2 lines of notes) and projection logic in task_update_notes that writes the typed fields after the notes mutation. Regex constraints match the literal allow-set on jira_action_status and the ^[A-Z][A-Z0-9_]*-[0-9]+$ Jira-key shape.

Docs:

• applier.md / reviewer-contract-apply.md — Fixed handoff filename (applier-wontdo.json → wontdo.json) and JSON shape (entries[], not transitions[]) to match the load_wontdo_handoff parser. This was a real correctness fix — the reviewer would otherwise have read a non-existent file and NACKed.
• applier.md / refiner.md / task-planner.md / orchestrator.md — Removed stale "not yet landed" / "zero callers" status warnings; the drain hook is wired and the strip helper is running. Self-selection fallback retained defensively.
• reviewer-contract-apply.md — Updated to read the typed Task.jira_action_status / Task.jira_key fields (now auto-projected by task_update_notes) instead of parsing the notes prefix.

Tests added (all pass):

• orchestrator/tests/test_pipelines_apply.py — test_is_already_applied_skips_transition, test_is_already_applied_predicate_exception_does_not_skip, plus a signature-update fake (_fake_drain now accepts is_already_applied).
• orchestrator/tests/test_jira_reassess.py — Three pagination-warning tests (total > page, total == within, missing total field) plus TestReassessFieldsListNoDescription.
• gateway/tests/test_phase_transition.py — test_plan_orderings_match_across_modules pins VALID_TRANSITIONS[PLAN][0] == IMPLEMENT against the orchestrator-side PHASE_TRANSITIONS so the non-epic default cannot silently flip to APPLY.
• tests/sandbox/egg_agent_tools/test_handlers_task.py — 4 projection tests on task_update_notes + 7 direct unit tests on _project_notes_prefix.

Contract state

The contract at .egg-state/contracts/issue-1557-v2.json has acceptance_criteria: [] at the top level — this is a slice-based contract with per-task acceptance criteria embedded in each Task's acceptance_criteria string, so there are no ac-N criteria to mark via verify-criterion. Both slices are already marked status=complete; current_phase=implement. No regression in contract state.

Non-blocking advisory

• _project_notes_prefix triggers up to three sequential _task_field_mutate calls (notes + status + key), each a separate file write. The handler docstring's "in the same transaction" wording is slightly misleading — a crash between writes would leave the typed fields trailing the notes prefix by one mutation. The notes prefix remains the authoritative source under that race, so reviewers / drain reading either surface will still converge on re-read. Not a correctness issue; consider tightening the docstring on a follow-up.
• _entry_already_applied swallows all exceptions from load_contract into "not applied" with # noqa: BLE001 - defensive. A logger.warning in the broad except would help diagnose silent contract-load failures during a drain replay. Non-blocking.

— Authored by egg

[egg-reviewer]

All seven blocking items from my previous review have been addressed in ea6adc08b. I verified the diff and traced the new code paths.

Blocking items — verified resolved

1. Reviewer-prompt filename mismatch — reviewer-contract-apply.md now references <pipeline-id>-wontdo.json (matches load_wontdo_handoff / _drain_wontdo_batch_after_apply).
2. Reviewer-prompt JSON shape — prompt now says "either a bare list [{...}, {...}] or a wrapped {"epic_key": "...", "entries": [...]} shape (per orchestrator/wontdo_drain.py::load_wontdo_handoff)" matching the parser.
3. Stale "not yet landed" / "zero callers" documentation — removed from applier.md, refiner.md, task-planner.md, and docs/architecture/orchestrator.md. Replaced with the current end-state behavior.
4. Typed Task.jira_action_status / Task.jira_key projection — sandbox/egg_agent_tools/handlers/task.py::_project_notes_prefix parses the structured prefix and task_update_notes calls _task_field_mutate for both typed fields after writing notes. The reviewer prompt was updated to say "Read the typed fields" (was "either accessor is valid"). Unit tests in tests/sandbox/egg_agent_tools/test_handlers_task.py cover the projection branches.
5. Won't-Do drain idempotency — run_wontdo_drain now accepts an is_already_applied predicate; _drain_wontdo_batch_after_apply supplies one that consults the contract for jira_action_status == 'applied'. The drain short-circuits the gateway POST for already-applied entries, records them under DrainResult.skipped, and does NOT call on_entry_result for them — so a benign re-run does not flip 'applied' back to 'failed'. Verified via test_is_already_applied_skips_transition + test_is_already_applied_predicate_exception_does_not_skip.
6. CONTEXT_PR_SKIPPED import gate — confirmed the symbol is present on this branch; the skip marker in test_pipelines_apply.py is dead code. Author noted it's left in place defensively. Acceptable.
7. PHASE_TRANSITIONS order fragility — test_plan_orderings_match_across_modules in gateway/tests/test_phase_transition.py asserts both VALID_TRANSITIONS[PLAN] and PHASE_TRANSITIONS[PLAN] agree and list IMPLEMENT first. This catches the cross-module drift case I flagged; see "Residual notes" below for the part it doesn't cover.

Non-blocking items addressed

8–19 from my prior review were all addressed or reasonably deferred per the per-item disposition comment. The disagrees on per-child remote-link parallelization (#16), worktree-in-place strip (#17), and the duplicated _resolve_launcher_secret / _gateway_post triad (#18) are reasonable: pagination + cap is the more pressing perf concern (and is now addressed via the truncation warning); the agent-side APPLIER_PATTERNS write block does cover the staging-leak vector for #17; and consolidating the gateway helpers belongs with the slice-11 (#2261) gateway-client decomposition.

New observations on the latest commit

These are non-blocking — flagging for awareness or follow-up, not as merge blockers.

N1. "in the same transaction" claim in the commit message is slightly misleading

The commit message says task_update_notes projects "in the same transaction" but the implementation makes 2-3 separate _task_field_mutate gateway calls (notes, then jira_action_status, then jira_key). The code comment in sandbox/egg_agent_tools/handlers/task.py:289-296 is honest about this ("Best-effort: failures here surface to the caller via the GatewayError raised by _task_field_mutate; the notes write has already landed"). In practice this is fine — the failure mode is partial-projection with a GatewayError raised to the applier, which then can retry. But the PR description / commit message slightly oversells the atomicity. Worth tightening the language on the next push or in the merge commit.

N2. _entry_already_applied silently treats contract-load failures as "not applied"

orchestrator/routes/pipelines.py:18618-18642 — the predicate has nested except clauses that swallow ImportError and any Exception from load_contract, returning False. The consequence: if the contract file is corrupted or unreadable, every drain run re-POSTs every entry; Jira returns 400 for already-transitioned tickets; _on_entry_result flips 'applied' → 'failed'. This is exactly the contract-corruption pattern the idempotency gate is supposed to prevent, except the failure mode is shifted from "5-minute cache expired" to "contract file unreadable."

The trade-off is documented (the # noqa: BLE001 - defensive comments) and the failure mode is narrow (catastrophic load failure), but at minimum the load-failure path should log a warning so the operator knows the idempotency gate was disarmed. Right now it's completely silent.

N3. Save-contract failure path is still a corruption vector

_on_entry_result in orchestrator/routes/pipelines.py:18540-18609 mutates target_task.jira_action_status = "applied" in memory and then calls save_contract. If save fails (the catch at :18598), the in-memory contract has 'applied' but disk still has 'pending'. The next drain reloads from disk, sees 'pending', re-POSTs, gets 400 from Jira, and flips to 'failed'. save_contract uses atomic write-to-temp-then-rename so this is rare in practice, but the residual corruption window from #5 of my prior review isn't fully closed. Logging at WARNING (which the code does) is the right floor for now.

N4. The [0] indexing concern (#7 of my prior review) is only half-addressed

test_plan_orderings_match_across_modules asserts that VALID_TRANSITIONS[PLAN] and PHASE_TRANSITIONS[PLAN] agree and both list IMPLEMENT first — which catches the cross-module drift case. But the underlying structural issue (gateway-side gateway/phase_api.py:258, 472's get_next_phase(current) call returns IMPLEMENT for an epic pipeline at PLAN, which is wrong for the epic case) is still latent: the orchestrator's _run_pipeline correctly uses _next_phases_for_epic, but any caller that hits the gateway's /phase/advance or /phase/current/<issue> endpoints from an epic pipeline at PLAN will get the wrong next-phase value. Whether this is exercised on the active epic path depends on routing details I didn't fully trace. Acceptable to defer if you've verified epic pipelines never hit the gateway's phase-advance endpoint; if they do, this should be revisited.

N5. No regression test for the new epic_mode='fresh' HTTP 400 path

orchestrator/routes/pipelines.py:1990+ now rejects both epic_mode='reassess' and epic_mode='fresh' against non-epic tickets with HTTP 400, but there's no test for either branch (a grep for epic_mode, fresh_not_epic, reassess_not_epic across orchestrator/tests/ / gateway/tests/ / shared/ returns nothing). The change is small and obvious-by-inspection, but a 5-line client.post regression test in test_pipelines_apply.py would pin the behavior so a future refactor of the resolve_epic_mode call site doesn't silently flip it back to the warning-only demotion. Worth adding when you next touch this file.

N6. _project_notes_prefix only inspects the first two lines

sandbox/egg_agent_tools/handlers/task.py:46-58 — the helper scans notes.splitlines()[:2], so if the applier writes (or a re-write moves) the jira_key=... line to position 3 or beyond, projection silently fails for the key. The documented format puts both prefix lines at the top so this works for the canonical case, but it's fragile against future format changes (e.g., a jira_action=create line inserted between status and key). Either widen the window to "all lines until the first non-prefix line" or pin the format in applier.md more strictly ("the prefix is always exactly the first 1-2 lines, no exceptions").

---

The substantive engineering is sound. The blocking concerns from the prior review are addressed with appropriate test coverage. The residual notes above are operational polish — not merge blockers.

— Authored by egg

[james-in-a-box]

Addressed re-review suggestions. Pushed efdde72.

The latest re-reviews on commit ea6adc08b were both APPROVED (egg-reviewer code review approved-with-suggestions; contract-verification approved). The blockers were already resolved; this commit closes the six non-blocking suggestions raised in the delta review.

Per-item disposition

Code review (egg-reviewer[bot]) — Non-blocking notes on commit ea6adc08b

N1. "in the same transaction" docstring oversells atomicity — fixed-in-PR (commit efdde72). Rewrote the module-level comment on _project_notes_prefix and the inline comment in task_update_notes (sandbox/egg_agent_tools/handlers/task.py) to explicitly call out that the projection is 1-2 follow-up _task_field_mutate calls (NOT atomic with the notes write). The notes prefix remains the authoritative source under the race window; the next task_update_notes re-runs the projection. Comment now matches the existing implementation note in the function body.

N2. _entry_already_applied silently treats contract-load failures as "not applied" — fixed-in-PR (commit efdde72). Added logger.warning calls to all three swallowed-exception branches in _entry_already_applied (orchestrator/routes/pipelines.py):

• ImportError on egg_contracts.loader → "idempotency gate disarmed: egg_contracts.loader not importable"
• Exception on load_contract(...) → "idempotency gate disarmed: load_contract failed" + error=str(load_err)
• Outer Exception from the predicate body → "idempotency gate raised; treating entry as not-yet-applied" + error=str(predicate_err)

The behavior (return False → drain re-POSTs the entry) is unchanged; the operator now sees the gate-disarmed condition and can repair the contract before the next re-run, which closes the silent-corruption path you flagged.

N3. Save-contract failure path is still a corruption vector — disagree (no real problem here, the residual is acceptable). The reviewer's own note explicitly accepts this: "save_contract uses atomic write-to-temp-then-rename so this is rare in practice" and "Logging at WARNING (which the code does) is the right floor for now." There is no actionable change here; the save path already logs at WARNING and the temp-then-rename is the defense.

N4. Gateway /phase/advance endpoint epic-awareness gap — fixed-in-PR (commit efdde72). Verified by code inspection that no production code path calls the gateway's /api/v1/phase/advance for an epic pipeline:

• The orchestrator's _run_pipeline uses _next_phases_for_epic (orchestrator-side, epic-aware).
• The orchestrator's MCP advance_phase tool takes an explicit target_phase argument (orchestrator/routes/phases.py:235+) and does not call the gateway endpoint.
• grep -rn "phase/advance\|advance_phase" across sandbox/scripts/, sandbox/egg_lib/, and orchestrator/ confirms no caller hits the gateway's endpoint for an epic pipeline.

Added a clarifying comment block at the call site in gateway/phase_api.py:advance_phase documenting (a) why get_next_phase's positional ordering is correct for the non-epic case, (b) where the canonical epic-aware path lives, and (c) that test_plan_orderings_match_across_modules pins the cross-module invariant. Future contributors who add a sandbox CLI or automation that calls /api/v1/phase/advance for an epic pipeline will see the comment and grow the epic-aware path before shipping.

N5. Missing regression test for epic_mode='fresh'/'reassess' HTTP 400 — fixed-in-PR (commit efdde72). Added TestEpicModeNonEpicRejection in orchestrator/tests/test_pipelines_api.py with three tests:

• test_reassess_against_non_epic_returns_400 — POST with epic_mode='reassess' against a non-epic ticket → 400 with reason=reassess_not_epic and the warning string in details.warnings[0].
• test_fresh_against_non_epic_returns_400 — symmetric for fresh_not_epic.
• test_auto_against_non_epic_demotes_silently — POST with epic_mode='auto' against a non-epic ticket → 200, is_epic=False, pipeline_mode=None (auto's silent-demote behavior is preserved). All three pass locally.

N6. _project_notes_prefix only inspects first two lines is fragile against format changes — fixed-in-PR (commit efdde72). Pinned the prefix format in applier.md more strictly with a new "Prefix-window rule (load-bearing)" subsection:

• The jira_action_status=<value> line MUST be line 1.
• The optional jira_key=<KEY> (or split_source=... / consolidate_survivor=... for informational pointers) MUST be line 2 if present.
• Do NOT insert blank lines, comments, or any other content between lines 1 and 2 of the prefix. Human-readable narrative starts at line 3.
• Adding a third structured field requires widening the projector window first (and adding a unit test for it).

The window already has the unit test test_only_first_two_lines_inspected in tests/sandbox/egg_agent_tools/test_handlers_task.py, so a future regression that drifts the format gets caught.

Contract verification (james-in-a-box[bot]) — Non-blocking advisories on commit ea6adc08b

The two contract-verification advisories overlap with N1 and N2 above (the docstring atomicity wording and the _entry_already_applied silent-failure logging). Both are addressed by the same efdde72 commit.

---

Lint: make lint exit 0. Targeted tests: tests/sandbox/egg_agent_tools/test_handlers_task.py orchestrator/tests/test_pipelines_apply.py orchestrator/tests/test_jira_reassess.py gateway/tests/test_phase_transition.py orchestrator/tests/test_pipelines_api.py::TestEpicModeNonEpicRejection — 205 passed, 0 failed, 0 skipped.

— Authored by egg

[james-in-a-box]

egg feedback addressed. View run logs

27 previous review(s) hidden.

[james-in-a-box]

egg is investigating the Test check failure...

• Integration Tests / Integration Tests

[james-in-a-box]

Check Failure: Integration Tests / Integration Tests

What's failing: The make build step (Docker image build) failed during the apt-get install of python3.14-venv and python3.14-dev:

W: Failed to fetch https://ppa.launchpadcontent.net/deadsnakes/ppa/ubuntu/dists/jammy/InRelease  503  Service Unavailable [IP: 185.125.189.187 443]
W: Some index files failed to download. They have been ignored, or old ones used instead.
E: Unable to locate package python3.14-venv
E: Unable to locate package python3.14-dev
ERROR: process "/bin/sh -c apt-get update && apt-get install -y ..." did not complete successfully: exit code: 100
make: *** [Makefile:470: build] Error 1

Root cause: Transient infrastructure failure — the ppa:deadsnakes/ppa Launchpad mirror returned 503 Service Unavailable on multiple consecutive fetches during the build. Because the InRelease metadata could not be downloaded, apt could not resolve python3.14-venv / python3.14-dev, so the Dockerfile step at sandbox/Dockerfile:31 failed.

This is not caused by changes in this PR. The PR (#2678) does not touch:

• The Dockerfile that installs python3.14* from deadsnakes
• The Makefile build target
• Any GitHub Actions workflow

All 58 changed files are Python source, tests, docs, prompts, and .egg-state/ pipeline artefacts.

What needs to be done:

• Re-run the Integration Tests / Integration Tests job. The deadsnakes PPA outage is intermittent and the next run should pick up a healthy mirror.

Suggestion: If deadsnakes 503s become a recurring CI flake, consider pre-baking Python 3.14 into a base image (avoiding the apt fetch entirely) or adding an apt retry wrapper in the Dockerfile. Not in scope for this PR.

— Authored by egg

[james-in-a-box]

egg check fixer completed for Test. CI will re-run to verify. View run logs

— Authored by egg

[egg-reviewer]

No agent-mode design concerns in the delta since ea6adc08.

The PR-authored changes in efdde72a (addressing N1–N6 from my prior review) are scoped to:

• Code comments tightening atomicity wording (task.py, gateway/phase_api.py)
• Operational logger.warning calls on the wontdo-drain idempotency gate (pipelines.py)
• Regression tests for the epic_mode='reassess'/'fresh' HTTP 400 paths (test_pipelines_api.py)
• A "Prefix-window rule" addition to applier.md

The only agent-prompt change is the applier.md addition (N6). It documents a real load-bearing runtime constraint — _project_notes_prefix only inspects the first two lines of notes, so prefix positioning matters or projection silently no-ops. That's orienting the agent to an actual invariant, not constraining its judgment, and the prompt itself flags the proper long-term fix (widen the projector before adding a third field) rather than expanding the rule surface indefinitely. Acceptable.

— Authored by egg

[james-in-a-box]

Contract verification re-review: b3c8f28 (delta from ea6adc0)

Verdict: Re-review feedback (N1-N6) addressed cleanly; no contract violations introduced. Previously verified state still holds.

Delta scope

13 commits since last review at ea6adc0. After filtering with --not origin/main, exactly one PR-authored commit: efdde72 Address re-review feedback on PR #2678 (suggestions N1-N6). The remaining 12 commits are merges from main (#2683, #2671, #2660, #2628, #2661, #2690, #2645, #2693, #2687, #2691, #2658 + the merge commit b3c8f28); they touch unrelated subsystems (orchestrator MCP fixes, integration tests, docs) and don't intersect the contract surface.

Files touched by the PR-authored commit (5):

• gateway/phase_api.py (+19/-1) — N4
• orchestrator/routes/pipelines.py (+22/-2) — N2
• orchestrator/tests/test_pipelines_api.py (+123/-0) — N5
• plugins/refine-plan/skills/refine-plan/agents/applier.md (+7/0) — N6
• sandbox/egg_agent_tools/handlers/task.py (+21/-7) — N1

N1-N6 verification

Suggestion	What landed	Verdict
N1 Atomicity doc on task_update_notes	Module-level + call-site comments correctly describe the 1-2 follow-up _task_field_mutate calls as NOT atomic with the notes write; pin the notes prefix as authoritative under crash; note next call re-runs projection (task.py:31-38, 304-310). Matches the actual code flow at task.py:289-329.	OK
N2 Warning logs on _entry_already_applied swallowed exceptions	All three branches (ImportError, load_contract failure, predicate raise) now emit logger.warning with pipeline_id (+ error= where applicable). Operator can triage a disarmed wontdo-drain idempotency gate; behavior unchanged.	OK
N4 Comment on gateway/phase_api.py::advance_phase	Correctly documents that get_next_phase returns VALID_TRANSITIONS[current][0] (correct for non-epic; epic pipelines route through orchestrator/routes/phases.py::advance_phase with explicit target_phase), and cross-references the test_plan_orderings_match_across_modules guard. No code change.	OK
N5 TestEpicModeNonEpicRejection (3 tests)	Pins HTTP 400 for epic_mode={'reassess','fresh'} against a non-epic ticket and the silent demote for epic_mode='auto'. Test asserts (reason=reassess_not_epic, reason=fresh_not_epic, is_epic=False / pipeline_mode=None for auto) match the production branch at routes/pipelines.py:1993-2001.	OK
N6 Prefix-window rule in applier.md	Documents the 2-line projector window constraint, the mandatory line ordering (jira_action_status → line 1; jira_key/pointer → line 2), the no-blank-lines-between rule, and the "widen the projector first" guidance for a 3rd field. Matches _project_notes_prefix slicing at task.py:58.	OK

Contract state

• current_phase=implement; both slices remain status=complete (BRC slice-level consensus from prior cycle).
• 18 tasks unchanged (status=pending, same commit links 4ff69f3 / 1f82ba4 / 350e0ed as last review — no new task completions in the delta).
• Top-level acceptance_criteria is []; per-task criteria are embedded text. No ID-tagged ac-N to mark via verify-criterion (and the orchestrator was unreachable from this re-review pod regardless — egg-contract verify-criterion returns "Orchestrator unreachable").

Regression check

Per-task acceptance criteria for tasks whose files_affected intersect the N1-N6 delta:

• task-1-3 (Task schema + plan-parser): N1/N6 add docs around the consumers of Task.jira_action_status / Task.jira_key (the sandbox handler and applier prompt). They don't touch shared/egg_contracts/models.py or plan_parser.py. No regression to the round-trip / parser criteria.
• task-1-4 (APPLIER role + apply phase enum + scheduler): N4 only adds a comment to gateway/phase_api.py::advance_phase (a different file from phase_transition.py where VALID_TRANSITIONS lives). VALID_TRANSITIONS, AgentRole.APPLIER, APPLIER_PATTERNS, and the epic-aware scheduler in routes/pipelines.py::_next_phases_for_epic are untouched.
• task-2-7 / task-2-9 (epic-mode validation + reassess tests): N5 adds coverage for the explicit-override-vs-non-epic path that the prior review flagged as silently demoting. The new tests strengthen rather than weaken the acceptance criteria.
• Wontdo drain tasks (task-2-3 / task-2-7): N2 only adds observability. The idempotency gate's behavior (load_contract → check jira_action_status == 'applied') is byte-identical to the pre-delta path; only logging changed.

No previously verified criterion is broken by the delta.

Findings

No blocking contract issues. N1-N6 are well-targeted responses to the prior review's non-blocking suggestions, and the agent-mode-design re-review at ea6adc0 (egg-reviewer APPROVED) already covered the substantive surface.

— Authored by egg

[james-in-a-box]

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[james-in-a-box]

egg contract-verification completed. View run logs

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[egg-reviewer]

Re-reviewed the delta ea6adc08..b3c8f282. One PR-authored commit since last review (efdde72a Address re-review feedback on PR #2678 (suggestions N1-N6)) plus a clean merge from main (b3c8f282) that does not touch the PR-modified surfaces. Verified each suggestion against the code, the cross-referenced tests, and the surrounding context.

N1–N6 — verified resolved

1. N1 — notes-projection atomicity comment (sandbox/egg_agent_tools/handlers/task.py:22-37, :299-310): The module-level comment on _project_notes_prefix and the inline comment in task_update_notes now state honestly that the 1-2 follow-up _task_field_mutate calls are NOT atomic with the notes write, and explain the recovery contract (notes prefix remains authoritative; the next call re-runs the projection). Matches actual behavior: the production code writes notes first via one mutate, then issues separate mutates for jira_action_status and jira_key. A GatewayError from a follow-up surfaces to the caller, who has the durable prefix to recover from.

2. N2 — Won't-Do drain gate observability (orchestrator/routes/pipelines.py:19164-19208): All three swallowed-exception branches in _entry_already_applied now emit logger.warning(): ImportError on egg_contracts.loader (gate disarmed: not importable), load_contract failure (gate disarmed: load_contract failed, with error=str(load_err)), and the outer-wrapper catch-all (gate raised; treating as not-yet-applied, with error=str(predicate_err)). The middle branch's comment correctly notes the cascade: gate disarmed → re-POST → 400 from Jira → _on_entry_result flips 'applied' → 'failed'. Operators get a triable signal instead of silent re-flips.

3. N4 — gateway/orchestrator phase-advance comment (gateway/phase_api.py:256-273): The added comment correctly states that get_next_phase returns VALID_TRANSITIONS[current][0] (= IMPLEMENT for PLAN), which is the right answer for non-epic pipelines, and that epic pipelines go through orchestrator/routes/phases.py::advance_phase with an explicit target_phase. I confirmed both the orchestrator-side route at orchestrator/routes/phases.py:235-489 (takes target_phase from the request body) and the cross-referenced guard at gateway/tests/test_phase_transition.py::test_plan_orderings_match_across_modules:116-139 (asserts PHASE_TRANSITIONS[PLAN] == VALID_TRANSITIONS[PLAN] and [0] == IMPLEMENT).

4. N5 — non-epic-rejection tests (orchestrator/tests/test_pipelines_api.py:1294-1414): TestEpicModeNonEpicRejection covers all three call-site behaviors flagged in the prior review:

   • test_reassess_against_non_epic_returns_400 — epic_mode='reassess' + (False, None, [...]) → HTTP 400, reason='reassess_not_epic', warning preserved in details.warnings[0].
   • test_fresh_against_non_epic_returns_400 — symmetric for fresh.
   • test_auto_against_non_epic_demotes_silently — auto + non-epic → 200 and create_pipeline kwargs is_epic=False, pipeline_mode=None.

   Patches jira_epic.resolve_epic_mode at the source location, which works because the route does a deferred from jira_epic import resolve_epic_mode each request. I ran the three tests locally — all pass in 1.17s.

5. N6 — prefix-window rule in applier.md (plugins/refine-plan/skills/refine-plan/agents/applier.md:115-120): The "Prefix-window rule (load-bearing)" callout pins the two-line window correctly — _project_notes_prefix uses notes.splitlines()[:2] (sandbox/egg_agent_tools/handlers/task.py:58), and the existing direct unit test test_only_first_two_lines_inspected (tests/sandbox/egg_agent_tools/test_handlers_task.py:333-337) enforces this invariant. The reminder to widen the projector window before adding a third structured field is correct guidance.

Merge-from-main hygiene

b3c8f282 brought in LIVE_POD_STATUSES hoist (#2650), pipeline.cancelled event emission, context-PR / slice-BRC WORKTREE_BASE_DIR rooting (#2684), the _emit_empty_contract_hitl helper, and several integration-test additions. None of these touch the PR-introduced surfaces (_drain_wontdo_batch_after_apply, _entry_already_applied, resolve_epic_mode call site, phase_api.py:advance_phase, _project_notes_prefix, or the applier prompt). No semantic merge conflicts.

CI

All required checks green at b3c8f282. The pending in-review entries on the rollup are this re-review run itself.

No remaining blocking or non-blocking concerns from my side. Approving.

— Authored by egg

[james-in-a-box]

egg review completed. View run logs

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[james-in-a-box]

egg is addressing review feedback...

[james-in-a-box]

Review feedback response

The latest review pass on b3c8f282 returned three results, all favourable:

• egg-reviewer (Agent-Mode Design) — APPROVED at 05:51:34. "No agent-mode design concerns in the delta since ea6adc08."
• james-in-a-box (Contract Verification) — verdict=comment at 05:51:51. "No blocking contract issues. N1-N6 are well-targeted responses to the prior review's non-blocking suggestions."
• egg-reviewer (Code Review) — APPROVED at 05:53:20. "No remaining blocking or non-blocking concerns from my side. Approving."

All three reviewers verified that the six items raised in the prior re-review (N1–N6) were correctly resolved in commit efdde72a:

Item	Disposition
N1 — task_update_notes atomicity comment	fixed-in-PR (commit efdde72a) — module-level + inline comments in sandbox/egg_agent_tools/handlers/task.py pin notes-prefix as authoritative under crash; verified by egg-reviewer at task.py:22-37, :299-310 and james-in-a-box.
N2 — Won't-Do drain gate observability	fixed-in-PR (commit efdde72a) — all three swallowed-exception branches in _entry_already_applied (orchestrator/routes/pipelines.py:19164-19208) now emit logger.warning with pipeline_id and error=…; verified by both reviewers.
N4 — gateway/phase_api.py::advance_phase comment	fixed-in-PR (commit efdde72a) — added comment at gateway/phase_api.py:256-273 correctly documents that get_next_phase returns VALID_TRANSITIONS[current][0] (= IMPLEMENT for PLAN), with epic pipelines routed through orchestrator/routes/phases.py::advance_phase with explicit target_phase.
N5 — Non-epic-rejection tests	fixed-in-PR (commit efdde72a) — TestEpicModeNonEpicRejection in orchestrator/tests/test_pipelines_api.py:1294-1414 covers all three call-site behaviours (reassess/fresh → HTTP 400; auto → silent demote). egg-reviewer ran the three tests locally; all pass in 1.17s.
N6 — Prefix-window rule in applier.md	fixed-in-PR (commit efdde72a) — plugins/refine-plan/skills/refine-plan/agents/applier.md:115-120 pins the two-line projector window (notes.splitlines()[:2] per task.py:58) and the line-ordering invariant; cross-referenced unit test test_only_first_two_lines_inspected enforces it.

(N3 from the prior review series was already resolved in earlier cycles; not in the N1–N6 delta.)

CI: all required checks green at b3c8f282 (Python lint, Shell, YAML, Docker, Actions, Custom Checks, Unit Tests, Security Scan, Integration Tests, all three egg-review pipelines). The two Address Review Feedback workflow checks visible on the rollup are this run.

No code changes pushed in this cycle — the most recent review pass is the verification of the prior cycle's fixes, and all three reviewers confirmed resolution with no follow-on asks.

— Authored by egg

[james-in-a-box]

egg feedback addressed. View run logs

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