[trissim]

Coherent S1 pipeline checkpoint, normal current main356 integration complete and pushed at 237ce17. Conflict-free ordinary merge14e66ad42 joins reviewed bdfd and main3569105574cb707d75922dc165a313365e1bd33c. All eleven S1 production modules are byte-unchanged against reviewed ba3b1a. No new production edit or competing runtime change. Parent remains integration/shipment owner; CI deferred, no optional-CI wait.

Production deletion first: pipeline checkpoint deletes 525 lines against its integrated base. Draft/validate/source/artifact-plan/execution descend once through existing capability/output declarations, AutoRegisterMeta, DTO MRO and the existing generic codec. Replaced raw field/key readers, duplicate membership store/roster, raw diagnostic scanners and copied clipping are deleted. JSON extension metadata remains mappings; native serialized receipts and advertised outputContract=ExecutionJobRef remain exact. Persisted formats: none changed.

Shared implementation belongs to real owning ancestors: ExecutionJobRenderer over actual ExecutionJobIdentity (Ref and Status remain siblings), McpDevTypedOutputRenderer for decode/render/optional facts, TypedCompositeCommandSpec for composite rendering, CodeDocumentRenderOptions for clipping. Producer result-family membership derives from the existing ExecutionSessionService._submit_job annotation; the parallel union alias and presentation retry roster were deleted. Typed AgentError identity is traversed without serializing/rescanning JSON. No source-service/runtime or installed package change.

Concrete extension evidence: a new DTO subclass and capability work through unchanged ingress and generated consumers without registry/caller/roster edits. Independent renderer capabilities cooperate in both diamond orders; each capability and actual ancestor executes once, identity occurs once in MRO/derived views. Existing parser controls remain unchanged. Actual antipattern source review (BOUND-2, IMPL-12/13/14, MEMB/identity/TIME-9) and current archive authority are in docs/refactor/S1-mcp-result-owners.rst.

Current focused source sanity after normal356 merge: 37 PASS, 6.46s/259196 KiB RSS, CPU0/60s, existing interpreter/dependencies. Pipeline production ingress/rendering, new subclass and both diamond orders, transport failures and config regression. Complete log/XML plus build/CLI evidence: docs/refactor/S1-main-f24-integration-20261001.rst and receipts/S1-main-f24-integration-20261001.tar.gz. Historical full pipeline 39 checks and shared-owner 29 controls remain in receipts/S1-pipeline-20261001.tar.gz. Original bounded R0 PASS and full-context R1 INCOMPLETE evidence retain actual limits: no global R1 proof, guard exception or erased failure.

Parent reports installed live acceptance on exact eleven unchanged modules in paired e16/f24 wheel: human draft/config/add/validate/render/nonempty artifact-plan; execute-source --no-wait composite returned session-1/job-1; original native job COMPLETE, four CH1/2 Z1/2 outputs retain addresses/calibration, 32x32 native uint16 and exact 8x8 MCP samples for all four; separate compile-only job-2 COMPLETE. Parent owns original recordings, exact runtime close and merge decision. Public partial receipt s1-installed-20261001/CHECKPOINT.rst remains distinct from the subsequently reported native phase. No new biology/UI acceptance or global proof claim; source owner did not launch MCP/native/GUI.

Named remaining S1: config; knowledge/function/authoring; object-state; plate; viewer/runtime; UI/code-document/state-surface. Compact selected-workflow/action_result mismatch remains owned, not claimed accepted. Plate acquisition path defect #337 is implemented separately in draft #338. Generated catalog connection input projection defect has actual source-only help/argument-rejection reproduction and Arendt ownership in separate #339; no scope expansion or shipment blocker for334.

[trissim]

Installed S1 checkpoint, not full acceptance

Source3e0fa472c3733a139b0016b904985038c703ba4b normally combines public
334ba3b1a486 and main8c512d404. WheelSHA256:
b916414a099c6f73540862e59b31bc93f20fb91b32bc20534b4ba33aafbc8b9c.
Normal build8.83s,226MiB groupRSS,exit0. Local-no-index/no-deps install0.
Fresh installed-I-B imports and every11 changed production module byte
comparison pass:6.87s,238.95MiB,original bound512MiB/60s unchanged.
Original two administrative failures are preserved: a plain .pth path did
not process backing dependency .pth files (missing zmq); then parent probe
read result_types on the capability instead of its actual output_contract.
Existing site.addsitedir mechanism and actual result-family owner correct
the probe/environment. No product code was changed to hide either failure.

Original installed MCP shell73809 retained live.stdin/stdout/timing. Health
is0.8.7,56 resources ready,PID676564/start1790833157.6205592, no drift or
reconnect required; final health confirms the same original process. The
first-use/pipeline contexts and capability side effects were retrieved.
Actual in-memory pipeline-1 creation, validation and complete source rendering
succeed through exposed MCP. Validation warns pipeline_empty, as expected.
The rendered source contains PipelineConfig() plus pipeline_steps=[], not a
steps-only or separately configured document. Generic call intentionally
returns native JSON, not a human compact-rendering acceptance claim.

Prepared four-plane Opera fixture from prior own qualification was copied
byte-for-byte into this ledger's writable fixture-opera. The protected
original is unchanged. Both artifact-plan JSON and human compact command
succeed with complete four-plane source inventory, typed calibration,
zero steps/axes and no error/warning. This exercises actual installed transport,
ingress and the migrated ArtifactPlanInspection renderer, but not nonempty
step/materialization summaries or ExecutionJobRef/Status/native execution.

Original misuse evidence remains: parent guessed nonexistent create-pipeline,
validate-pipeline and render-pipeline-source CLI aliases. The actual command
help showed these capabilities require generic call; no product defect inferred.
The initial artifact-plan request targeting read-only prior fixture was
rejected by writable path policy. Staging an owned writable copy repaired
the target without changing roots, replaying an uncertain mutation or
bypassing the guard. All failures remain in the original transcript.

Original shell exited2 at2026-10-01T05:43:17Z. Its actual shell contract
retains earlier usage errors as aggregate exit2 despite subsequent success.
Original MCP676564 is absent and validation.lock is free. No native/viewer,
catalog preparation, biological work or source-bearing function registration
occurred. No new calls should reuse/replay this closed endpoint.

Next: normal integration of merged333/mainf24 and bounded native-backed draft,
compile/job and generated/human rendering acceptance using a separately named
original log sequence and explicit isolated catalogue-cache selector before
startup. Until then334 remains draft. Original R1 is incomplete, not waived;
full S1 and every original ZIP surface remain in the active goal.

[trissim]

S1 installed native entrypoint acceptance

Parent integration owner. Qualified source e16d74bd2baa909697953e22f692009106810155
normally combines public S1 ba3b1a4 and main
f24a828. Current worker integration 4be5af1
has no diff in openhcs, external, pyproject.toml, MANIFEST.in or installer
scripts against that candidate. Installed OpenHCS 0.8.7 wheel SHA-256:
d2652e48e9f241fc3cba6879398f0d19b9016d6f0d75ca4231e668de1497db39.
Actual installed imports and all eleven changed production modules matched.
The paired installed PolyStore version is 0.3.0. Heavy dependencies are backed
by the existing retained basicpy-live-candidate environment, not redownloaded.

Real continuous entrypoint journey

The original persistent dev-client shell 68677 launched MCP 693789 and exact
owned native 694124 on TCP 5993/ACK 6993. Original startup was observed to READY
without restart or replay; explicit catalogue preparation on that same owner
was READY. Health was current before and after the journey, with 56 packaged
resources ready and no stale source/reconnect required.

Real catalogue search and function description selected the existing OpenHCS
numpy Gaussian callable. Human composite draft-pipeline-step created, added,
validated and rendered a complete PipelineDocument. A separate reflected
pipeline config specified one worker, OpenHCS input and threading; ordinary
create/add/validate/render produced pipeline-2/step-2 with valid=true. Its
renderer_probe_pipeline.py is the MCP-rendered source plus one trailing newline.

Actual artifact-plan JSON and human compact rendering reported one R01C01
axis, one renderer_probe step, four source planes, worker_0, CH1/2 and Z1/2,
and main-flow persistence. This was a 32x32 synthetic engineering fixture,
not a biological analysis or held-out sample.

Actual human execute-source --no-wait on that exact endpoint returned
session-1/job-1 and native execution 1e548dc8-bccd-4b92-849a-87a126f0c77a.
The original job reached complete in 1.5693 seconds, error=null, one well.
Output inspection reopened four physical image files with their five-component
addresses and 1.1867525298988042 micrometer spacing retained. Native-resolution
MCP sampling of every output reported 32x32 uint16 and included an exact 8x8
sample. This proves bounded output transport/readability, not whole-array
numerical equivalence, cell counts or biological validity.

A separate compile-only job-2 used the same source-backed session and reached
complete in 0.4314 seconds, error=null. It did not repeat image execution.
The actual producer returned ExecutionJobRef and ordinary lifecycle status
ExecutionJobStatus; the human execute-source path exercised declaration-owned
decoded composite rendering. A live wait=true submission and live human
Status sibling rendering were not exercised by this journey.

Original limitations and failed inputs retained

The earlier live.stdin/live.stdout/live.timing are unchanged and include usage
errors; their shell exited 2. This original native phase exited 0. A mistaken
capability filter named workflow was ignored; the corrected workflow_group
filter returned the seven real execution tools. A first sample used unsupported
region field names, so returned the default 32x32 region and omitted values at
the 64-element limit. It was not an 8x8 witness; corrected documented y/x/
height/width requests produced the four actual 8x8 samples.

Read-only output inspection reported partial due to missing grid_dimensions
in this synthetic fixture's metadata; all four plane/address records parsed.
No UI PlateManager auto-add occurred, as expected for headless execution.
No desktop/GUI journey, complete S1/ZIP closure or completed global R1 proof is
claimed. The original full-context R1 remains INCOMPLETE, not waived or passed.
Generated start-function-catalog-preparation exposes no endpoint flags despite
its required connection contract; source owner Arendt has the follow-up.

Cleanup, resources and original evidence

Exact original bootstrap close was issued once. It reported acknowledged,
endpoint_terminated, process_exited and succeeded all true for 694124 at its
retained create_time. Parent independently confirmed that PID and both
listeners absent. Final health succeeded; original MCP/shell exited normally,
PIDs 693477/693789 disappeared and the validation flock became available.
Protected desktop :0, Xvfb/VNC :91 and current H002 :90/7790/5690 were retained.

Available RAM was about 20.5 GiB before execution; disk about 19.1 GiB. Swap
13.4 GiB was warning-only. One tiny threaded worker was used, no Fiji/JDK/model/
dataset download. Source checks/builds were separate from native memory budgets.
All scratch was archived in scratch-after-close.tgz; native tar comparison
returned zero before any disposal. All original recordings and build logs are
retained. Final original native.stdout SHA-256:
11fce498531bf97cddc56d7ccd6509ade3901a2af9877b2e058d3f5c2cd500b4.
Final original native.stdin SHA-256:
b6ae71a5723199806377f2079c011d91c1d8f4b89b76a28b1b1cf718cbd0c8ca.
Saved pipeline SHA-256:
4e6d98d5becde05d5537561a8eabe1ca7447b64eee4b564deb42ef2888154c50.

This is a shippable pipeline-rendering checkpoint, not completion of the active
goal. Fresh independent development-only blind analysis follows shipment;
held-out/reference answers remain sealed.

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