Namespace .egg-state files per-pipeline to prevent merge conflicts (#895)

* Initialize SDLC contract for issue #871

* Add refine analysis for issue #871

* Add agent-design review verdict for issue #871 refine phase

* Add refine review verdict for issue #871

* Persist statefiles after refine phase

* Add architect analysis for issue #871: namespace .egg-state files per-pipeline

* WIP: auto-commit uncommitted work (architect) [issue-871]

Container 43985389ec6a15b861158676d5595c1076f7306aa4b6048fc26c10298f8bf331 exited with uncommitted changes.
This commit preserves the agent's work-in-progress.

Authored-by: egg

* Add implementation plan for issue #871: namespace .egg-state files per-pipeline

* Add risk assessment for issue #871: namespace .egg-state files per-pipeline

* WIP: auto-commit uncommitted work (task_planner) [issue-871]

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This commit preserves the agent's work-in-progress.

Authored-by: egg

* WIP: auto-commit uncommitted work (risk_analyst) [issue-871]

Container d09dc3dd6da2090b5045cf58fa343e548d37e2f69c563d16e966a1959dbbacd4 exited with uncommitted changes.
This commit preserves the agent's work-in-progress.

Authored-by: egg

* Add plan review verdict for issue #871: needs_revision

* Revised architect output: address plan review feedback for issue #871

* WIP: auto-commit uncommitted work (architect) [issue-871]

Container 69ae9374a57d14f6288cea0f022be7439821623fd492b99e463f60eabc7dcaee exited with uncommitted changes.
This commit preserves the agent's work-in-progress.

Authored-by: egg

* Revised plan: address reviewer feedback on wrapper layer callsites

* WIP: auto-commit uncommitted work (task_planner) [issue-871]

Container f140cdb5bace1d4c87c8ed24976c41ec649692560a308ddc3ae4fe79f067fbb8 exited with uncommitted changes.
This commit preserves the agent's work-in-progress.

Authored-by: egg

* Risk assessment revision 2: identify plan draft sync gap and test scope corrections

* WIP: auto-commit uncommitted work (risk_analyst) [issue-871]

Container 90b2c25febc1000b81a154fdc49dca28e4d232862cb4e3f1642bbf208f62f694 exited with uncommitted changes.
This commit preserves the agent's work-in-progress.

Authored-by: egg

* Plan review: approved (revision 2)

* Persist statefiles after plan phase

* Namespace .egg-state files per-pipeline to prevent merge conflicts

Add issue/pipeline identifier prefix to all globally-named files in
.egg-state/agent-outputs/ and .egg-state/checks/, matching the convention
already used by contracts/, drafts/, and reviews/.

Core changes:
- shared/egg_contracts/orchestrator.py: Add optional identifier param to
  load_agent_output, save_agent_output, collect_handoff_data with fallback
- orchestrator/handoffs.py: Forward identifier through wrapper functions
- orchestrator/dispatch.py: Pass self.contract_key as identifier
- orchestrator/routes/signals.py: Derive identifier from pipeline
- orchestrator/routes/pipelines.py: Update prompt builders and readers
  to use prefixed filenames

* Add tests for namespaced .egg-state file paths

- test_pipeline_prompts.py: Update checker/check-and-fix result filename
  assertions to expect prefixed names; add TestNamespacedOutputFilenames
  class for agent prompt output paths; add _read_tester_gaps identifier
  tests for prefixed/fallback behavior
- test_orchestrator.py: New test file with 9 tests for load_agent_output,
  save_agent_output, and collect_handoff_data with identifier parameter
  (prefixed path, fallback, neither-exists, priority, string identifiers)
- phase-runner.sh: Derive identifier from EGG_ISSUE_NUMBER/EGG_PIPELINE_ID
  for namespaced implement-results.json filename

* Update docs and agent mode commands for namespaced filenames

Update all documentation and sandbox agent mode command files to reference
{identifier}-prefixed output filenames instead of global names. Includes
sdlc-pipeline.md, agent-development.md, orchestrator.md, all four agent
mode command files, and the phase_output.py docstring.

* Document agent-outputs namespacing and backward compat fallback

* Add gap-targeting tests for namespaced .egg-state file paths

* Fix remaining hardcoded tester-output.json paths and lint issues

* Update implement phase check results: all passed

* Persist statefiles after implement phase

* Address review feedback: extract _pipeline_identifier helper

- Extract repeated `issue_number if issue_number is not None else pipeline_id`
  pattern (11 occurrences) into a `_pipeline_identifier()` helper function
  to reduce divergence risk if the fallback logic changes.

- Fix inconsistent truthiness check in `_synthesize_plan_draft`: the prefixed
  file construction used `if _synth_id` (truthiness) instead of
  `if _synth_id is not None`, which was inconsistent with all other identifier
  checks. Now that the helper always returns `int | str`, the guard is
  unnecessary and has been removed entirely.

Authored-by: egg

---------

Co-authored-by: egg-orchestrator <egg@localhost>
Co-authored-by: jwbron <8340608+jwbron@users.noreply.github.com>
Co-authored-by: egg-reviewer[bot] <261018737+egg-reviewer[bot]@users.noreply.github.com>

Author: 4 people

.egg-state/agent-outputs/871-integrator-output.json

@@ -0,0 +1,54 @@
+{
+  "status": "success",
+  "tests": {
+    "total": 6692,
+    "passed": 6692,
+    "failed": 0,
+    "skipped": 85
+  },
+  "lint": {
+    "status": "pass",
+    "issues_found": 3,
+    "issues_fixed": 3,
+    "details": "Removed unused pytest imports from test_handoffs_namespaced.py and test_orchestrator.py; fixed import sort order in test_handoffs_namespaced.py; reformatted 5 files via ruff format"
+  },
+  "integration_issues": {
+    "found": 2,
+    "fixed": 2,
+    "details": [
+      {
+        "file": "orchestrator/routes/pipelines.py",
+        "line": 2213,
+        "issue": "Hardcoded tester-output.json in _build_phase_prompt revision instructions not updated to use namespaced path",
+        "fix": "Updated to use f-string with {issue_number if issue_number is not None else pipeline_id}-tester-output.json"
+      },
+      {
+        "file": "orchestrator/routes/pipelines.py",
+        "line": 2810,
+        "issue": "Hardcoded tester-output.json in _build_phase_scoped_prompt revision checklist not updated to use namespaced path",
+        "fix": "Updated to use f-string with {pipeline.issue_number if pipeline.issue_number is not None else pipeline_id}-tester-output.json"
+      }
+    ]
+  },
+  "regressions": {
+    "found": false,
+    "details": "All 6692 existing tests pass. No regressions detected."
+  },
+  "summary": "Integration verified successfully. The coder's implementation correctly namespaces .egg-state files per-pipeline to prevent merge conflicts. Two hardcoded tester-output.json references in prompt-building functions were missed by the coder and have been fixed by the integrator. All tests pass and lint is clean after fixes.",
+  "changes_reviewed": {
+    "core_library": "shared/egg_contracts/orchestrator.py - load_agent_output, save_agent_output, collect_handoff_data now accept identifier parameter with backward-compat fallback",
+    "orchestrator_handoffs": "orchestrator/handoffs.py - wrapper functions forward identifier to core library",
+    "pipeline_routes": "orchestrator/routes/pipelines.py - all callers pass identifier derived from issue_number or pipeline_id; prompt builders reference namespaced filenames",
+    "signals": "orchestrator/routes/signals.py - complete signal handler passes identifier when saving agent output",
+    "docs": "docs/architecture/orchestrator.md, docs/guides/agent-development.md, docs/guides/sdlc-pipeline.md - updated to reference namespaced filenames",
+    "agent_modes": "sandbox/.claude/commands/{coder,tester,documenter,integrator}-mode.md - updated output filename instructions",
+    "tests": "orchestrator/tests/test_handoffs_namespaced.py (new), shared/egg_contracts/tests/test_orchestrator.py (new), orchestrator/tests/test_pipeline_prompts.py (extended) - comprehensive coverage of namespaced paths, backward compat, edge cases"
+  },
+  "commit": "fbf79998f",
+  "acceptance_criteria": {
+    "all_egg_state_files_namespaced": true,
+    "no_globally_named_files_remain": true,
+    "backward_compatible_reader": true,
+    "documentation_updated": true
+  }
+}

.egg-state/agent-outputs/architect-output.json

@@ -4,12 +4,12 @@
     {
       "name": "lint",
       "passed": true,
-      "output": "==> Ruff check...\nAll checks passed!\n==> Ruff format check...\n429 files already formatted\n==> Mypy...\nSuccess: no issues found in 118 source files\n==> Shellcheck...\n==> Custom checks... all passed"
+      "output": "==> Ruff check...\nAll checks passed!\n==> Ruff format check...\n430 files already formatted\n==> Mypy...\nSuccess: no issues found in 118 source files\n==> Shellcheck...\n==> Yamllint...\nSKIP: yamllint not installed\n==> Hadolint...\nSKIP: hadolint not installed\n==> Actionlint...\nSKIP: actionlint not installed\n==> Custom checks...\n  bin-symlinks...\nOK: All 2 bin/ symlinks are valid\n  claude-imports...\nWarning: host-services directory not found\n  container-host-boundary...\nOK: No forbidden host-services imports found in sandbox\n  container-paths...\nOK: No problematic sys.path patterns found\n  docker-and-claude-invocations...\nOK: No docker/claude invocation violations found\n  gh-cli-usage...\nWarning: host-services directory not found\n  hardcoded-ports...\nOK: No hardcoded port numbers found\n  llm-api-calls...\nOK: No direct LLM API usage found outside sandbox\n  model-versions...\nOK: No non-alias Claude model references found\n  reviewer-job-names...\nOK: All reviewer jobs use the required naming prefix\n  workflow-secrets...\nOK: No untrusted script execution with secrets found in workflows"
     },
     {
       "name": "test",
       "passed": true,
-      "output": "=========== 6685 passed, 85 skipped, 4 warnings in 73.80s (0:01:13) ============\n\nFixed: 2 docker_client test failures caused by sys.modules mock pollution from test_checkpoint_discovery.py. Added early docker import in orchestrator/tests/conftest.py to ensure real docker module is in sys.modules before test collection."
+      "output": "==> Running unit tests...\npytest tests/ gateway/tests/ orchestrator/tests/ -v\n6692 passed, 85 skipped, 4 warnings in 73.24s (0:01:13)"
     },
     {
       "name": "security",