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fix: reconcile generated organ guidance with the body map #497
Description
Overview
Reconcile generated repository guidance with the existing Mind body map. Fresh Heart evidence reports 18 mismatches; DNA missing guidance/hooks already landed in DNA#1 and its clean local checkout has now been synchronized. Remaining generated maps/tables are stale on origin/main.
Plan
- Create isolated worktrees from current remote main for the affected guidance consumers.
- Add Broca's required generator markers; run only applicable canonical repos_sync generators for maps, deliverable/filing blocks and public tables.
- Add Broca/DNA links to the hub's existing organism prose and regenerate the unversioned workspace root routing table.
- Validate the generated surfaces and diff scope; preserve all domain code, dirty canonical work and Scientist/Broca plans.
- Open one small PR per affected repository and retain the incident evidence in Mind.
Tier: judge — merge mode: human /prm. No merge/release/rehearsal.
Detailed implementation plan and branch survey
Branch: feature/heart-manifest-drift. Worktree root: /home/jammy/Code/PyAutoLabs/.worktrees/heart-manifest-drift.
Repositories: PyAutoBroca, PyAutoDNA, PyAutoCortex, PyAutoEyes, PyAutoEars, PyAutoPulse, PyAutoInsight, PyAutoNerves, PyAutoGut, PyAutoScientist, .github, pyautolabs.github.io.
All canonical checkouts are on main except .github's already-merged feature/search-ext-b1-registration. Cortex has 4 dirty science files; Eyes 3 untracked data/output/script paths; Gut 4 untracked caches. All are preserved. Independent Pulse ledger PR #48 remains untouched. No active Mind claims cover the target repositories.
Edits: AGENTS.md generated blocks only in organs, README.md generated organ table only in Scientist, profile/README.md table in .github, index.html organism blurb in hub. Root AGENTS routing block is a local unversioned generated surface.
Use repos_sync.py --root with bounded --only/--repo options. Never run unrestricted generation across symlinked canonical repositories. Replace root AGENTS symlink with a task-local copy before task generation. Validate full generated checks against task bundle and inspect exact diffs. No new tests for deterministic prose regeneration; run existing relevant generator checks and required repo checks where applicable.
Live Heart RED authorization
Exact reason: release validation FAILED (stage integrate).
User authorized the three named repair scopes on 2026-10-10: “yeah I authorize, fix the bugs and ensure when we continue work on the epic it knows this owkr happened but just get the fixes sorted for now”. This manifest task is independent of that release failure and uses development-only authorization; it must not claim to repair the integration failure. Existing validation/check protections remain mandatory.
Original prompt
Starting prompt
Reconcile the current generated-guidance manifest drift
Type: bug
Target: health_fixes
Autonomy: supervised
Consequence: judge
Priority: high
Status: draft — blocked at Heart RED entry gate
Primary repository: @PyAutoMind.
Incident evidence (2026-10-10)
Health workflow then bug health completed. Supported vitals tick ingested release-integrate
https://github.com/PyAutoLabs/PyAutoHeart/actions/runs/38038078541 .
Heart at 2026-10-10T16:21:14.391928+00:00: RED, score 60; exact release RED:
release validation FAILED (stage integrate).
Version 2026.10.10.1.dev81101: 726 passed, 2 failed, 85 skipped, zero timeouts;
installation A–F passed. Same two failures recur from run 37907620652.
Local evidence: workspace-root tmp/heart-red-investigation/ (artifacts, logs,
status-refreshed.json, health-refreshed.json, door.json).
Workflow boundary
Draft only. start-dev step 0a stopped at Heart RED before planning, issue creation,
claims or source edits. Requires live scoped RED authorization. No merge or release
is authorized. Preserve Scientist adoption and Broca expansion plans. Recheck claims
and remote refs before starting. Do not modify other sessions' worktrees.
Bounded defect and owner
Independent of the PyAutoFit search refactor. Fresh Heart tick still reports eight
yellow reason categories / 18 concrete mismatches:
- PyAutoBroca: missing end-at-deliverable and where-to-file blocks.
- PyAutoDNA: three missing Claude hook/settings files and missing AGENTS guidance.
- Hub index: Broca and DNA absent from organism blurb.
- Stale organism maps: Cortex, Eyes, Ears, Pulse, Insight, Nerves, Gut.
- Stale public tables: org .github/profile/README.md and Scientist README.md.
- Root AGENTS routing table stale.
Before any repair, fetch each owning repository, read its guidance, compare remote
main and local dirty/claimed files, and identify existing registration work. Fresh
local drift is proven; whether each mismatch needs a PR versus safe checkout
synchronization remains unverified. Do not bulk-write across canonical checkouts:
Cortex/Eyes/Gut already have local modifications. No edits to Scientist adoption or
Broca expansion plans. Split owner-specific changes as needed; use canonical
repos_sync generation and its checks, not hand-written generated content.
Acceptance: current remote source and local checkout state explained, generated
checks pass without suppression, supported Heart tick removes these warnings.
Requires development-only RED authorization for this non-RED corrective scope.
Original user request (verbatim)
Investigate and resolve the current PyAutoHeart RED before we resume the PyAutoScientist adoption pilot. Use the health workflow first, then the bug/start-dev workflow for any fixes.
Fetch the relevant repositories, read their AGENTS.md instructions, and inspect Heart’s latest authoritative verdict and underlying evidence. Distinguish current failures from stale evidence, expected in-progress work, and unrelated problems.
Specifically check whether the failures are caused by, or already being addressed by, the ongoing PyAutoFit refactor. Find its Mind task records, issues, branches, worktrees, PRs and CI results. Trace each relevant Heart failure to concrete evidence; do not assume the refactor explains everything. Avoid duplicating work, modifying its claimed worktrees, or interfering with another session.
Briefly report each RED reason, its likely cause, related existing work, and the next action. If the refactor already covers a failure, record that dependency and identify what completion or validation will clear it. For independent failures, create bounded tasks and implement the necessary fixes through the existing workflow. Make routine decisions autonomously; ask only for genuine blockers or required Heart RED authorization, quoting the exact reasons and requested scope.
Refresh Heart through its supported procedures after fixes or completed upstream work. Do not suppress failures, weaken checks, or mark unresolved evidence green. Finish with the authoritative verdict, validation evidence, remaining blockers, and whether the Scientist dashboard phase can start.
Leave the Scientist adoption and Broca expansion plans unchanged during this work. Their implementation resumes after Heart is sorted
Activity
Jammy2211 commentedon Oct 10, 2026
Overview
Reconcile generated repository guidance with the existing Mind body map. Fresh Heart evidence reports 18 mismatches; DNA missing guidance/hooks already landed in DNA#1 and its clean local checkout has now been synchronized. Remaining generated maps/tables are stale on origin/main.
Plan
Tier: judge — merge mode: human /prm. No merge/release/rehearsal.
Detailed implementation plan and branch survey
Branch: feature/heart-manifest-drift. Worktree root: /home/jammy/Code/PyAutoLabs/.worktrees/heart-manifest-drift.
Repositories: PyAutoBroca, PyAutoDNA, PyAutoCortex, PyAutoEyes, PyAutoEars, PyAutoPulse, PyAutoInsight, PyAutoNerves, PyAutoGut, PyAutoScientist, .github, pyautolabs.github.io.
All canonical checkouts are on main except .github's already-merged feature/search-ext-b1-registration. Cortex has 4 dirty science files; Eyes 3 untracked data/output/script paths; Gut 4 untracked caches. All are preserved. Independent Pulse ledger PR #48 remains untouched. No active Mind claims cover the target repositories.
Edits: AGENTS.md generated blocks only in organs, README.md generated organ table only in Scientist, profile/README.md table in .github, index.html organism blurb in hub. Root AGENTS routing block is a local unversioned generated surface.
Use repos_sync.py --root with bounded --only/--repo options. Never run unrestricted generation across symlinked canonical repositories. Replace root AGENTS symlink with a task-local copy before task generation. Validate full generated checks against task bundle and inspect exact diffs. No new tests for deterministic prose regeneration; run existing relevant generator checks and required repo checks where applicable.
Live Heart RED authorization
Exact reason:
release validation FAILED (stage integrate).User authorized the three named repair scopes on 2026-10-10: “yeah I authorize, fix the bugs and ensure when we continue work on the epic it knows this owkr happened but just get the fixes sorted for now”. This manifest task is independent of that release failure and uses development-only authorization; it must not claim to repair the integration failure. Existing validation/check protections remain mandatory.
Original prompt
Starting prompt
Reconcile the current generated-guidance manifest drift
Type: bug
Target: health_fixes
Autonomy: supervised
Consequence: judge
Priority: high
Status: draft — blocked at Heart RED entry gate
Primary repository: @PyAutoMind.
Incident evidence (2026-10-10)
Health workflow then bug health completed. Supported vitals tick ingested release-integrate
https://github.com/PyAutoLabs/PyAutoHeart/actions/runs/38038078541 .
Heart at 2026-10-10T16:21:14.391928+00:00: RED, score 60; exact release RED:
release validation FAILED (stage integrate).Version 2026.10.10.1.dev81101: 726 passed, 2 failed, 85 skipped, zero timeouts;
installation A–F passed. Same two failures recur from run 37907620652.
Local evidence: workspace-root
tmp/heart-red-investigation/(artifacts, logs,status-refreshed.json, health-refreshed.json, door.json).
Workflow boundary
Draft only. start-dev step 0a stopped at Heart RED before planning, issue creation,
claims or source edits. Requires live scoped RED authorization. No merge or release
is authorized. Preserve Scientist adoption and Broca expansion plans. Recheck claims
and remote refs before starting. Do not modify other sessions' worktrees.
Bounded defect and owner
Independent of the PyAutoFit search refactor. Fresh Heart tick still reports eight
yellow reason categories / 18 concrete mismatches:
Before any repair, fetch each owning repository, read its guidance, compare remote
main and local dirty/claimed files, and identify existing registration work. Fresh
local drift is proven; whether each mismatch needs a PR versus safe checkout
synchronization remains unverified. Do not bulk-write across canonical checkouts:
Cortex/Eyes/Gut already have local modifications. No edits to Scientist adoption or
Broca expansion plans. Split owner-specific changes as needed; use canonical
repos_sync generation and its checks, not hand-written generated content.
Acceptance: current remote source and local checkout state explained, generated
checks pass without suppression, supported Heart tick removes these warnings.
Requires development-only RED authorization for this non-RED corrective scope.
Original user request (verbatim)
Investigate and resolve the current PyAutoHeart RED before we resume the PyAutoScientist adoption pilot. Use the health workflow first, then the bug/start-dev workflow for any fixes.
Fetch the relevant repositories, read their AGENTS.md instructions, and inspect Heart’s latest authoritative verdict and underlying evidence. Distinguish current failures from stale evidence, expected in-progress work, and unrelated problems.
Specifically check whether the failures are caused by, or already being addressed by, the ongoing PyAutoFit refactor. Find its Mind task records, issues, branches, worktrees, PRs and CI results. Trace each relevant Heart failure to concrete evidence; do not assume the refactor explains everything. Avoid duplicating work, modifying its claimed worktrees, or interfering with another session.
Briefly report each RED reason, its likely cause, related existing work, and the next action. If the refactor already covers a failure, record that dependency and identify what completion or validation will clear it. For independent failures, create bounded tasks and implement the necessary fixes through the existing workflow. Make routine decisions autonomously; ask only for genuine blockers or required Heart RED authorization, quoting the exact reasons and requested scope.
Refresh Heart through its supported procedures after fixes or completed upstream work. Do not suppress failures, weaken checks, or mark unresolved evidence green. Finish with the authoritative verdict, validation evidence, remaining blockers, and whether the Scientist dashboard phase can start.
Leave the Scientist adoption and Broca expansion plans unchanged during this work. Their implementation resumes after Heart is sorted
Jammy2211 commentedon Oct 10, 2026
Repair ready for human merge review
All 12 bounded guidance PRs are open:
022f16a7c154)fa62b4b558f4)9297735c44ec)8e1ac3b1989b)b59f5662c309)6ce55c32456b)dd0b592c042d)52cd34ad2988)64a23441789d)1c88d232cca1)cb2dd954125b)ee3cea100c7c)Validation: full canonical repos_sync --check passes in the isolated task bundle; 57 generator tests; Broca 19 tests + registry/render; DNA 18; Ears 126; Eyes 87 + Ruff + all 265 live figure URLs; Insight 183 + Ruff/offline; Pulse 206 + Ruff/offline; Nerves 241; hub 9. Independent review CLEAN verifies exact generated content and preservation outside allowed blocks. Lychee is unavailable locally; Eyes link checking remains a CI gate. No functional source or Scientist/Broca plan changed.
DNA’s already-merged #1 was safely fast-forwarded in its clean canonical checkout. The unversioned root AGENTS routing table was regenerated locally. Dirty canonical Cortex/Eyes/Gut content and all other sessions were preserved. The task-created undeclared survey symlink was removed from this task bundle only; the survey checkout itself is untouched.
Live user authorization (2026-10-10), after exact RED
release validation FAILED (stage integrate)and the named scopes: “yeah I authorize, fix the bugs and ensure when we continue work on the epic it knows this owkr happened but just get the fixes sorted for now”. This non-causal manifest repair uses development-only RED authorization. No merge/release/rehearsal. CI/merge status must be judged at the exact heads before merging.Heart refreshed at 2026-10-10T16:34:35.998805+00:00 remains RED 60. Local canonical drift fell from 18 to 14 mismatches (five warning categories); the remaining files are intentionally in unmerged PRs. After merge, safely synchronize clean checkouts or coordinate dirty ones and tick Heart again. The two release-integration failures are separately repaired in autofit_workspace_test#110 and autolens_workspace#589. Fresh supported wheel integration is still required before GREEN; no evidence was suppressed.
Jammy2211 commentedon Oct 10, 2026
heart-manifest-drift
Shipped: all twelve PRs merged under human
/prm. Every configured head-SHA Actions run and test job passed. Cortex, .github and public hub had no checks; human explicitly authorized all three after disclosure. Broca PR deployment skipped by design; build and both test runs passed. Every claimed branch has zero unmerged commits against origin/main.Restored canonical generated policy/maps/tables and public organ links. No Scientist adoption or Broca expansion plan changes. DNA missing guidance had already shipped in DNA#1; that checkout was synchronized. This task fixes independent manifest warnings, not the release integration failure.
Validation: complete task-bundle repos_sync check PASS; 946 existing tests PASS; Eyes 265 live URLs PASS; independent CLEAN review verified exact canonical generated blocks and no unrelated edits. Two workspace RED causes shipped separately in heart-fitness-dispatch and heart-hierarchical-backend. Heart's failed release evidence still requires fresh supported integration validation; no release/rehearsal is authorized.
Generator trap: --only does not bound every repos_sync generator. Applied canonical generators only to asserted claimed paths; did not modify another session's claimed worktree or retained output. The undeclared COWLS symlink was removed only from this task bundle, preserving its source checkout.