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Addresses #540: executable pixel-space rooted neurite workflow

Ready: source, ordinary whole-installed and actual public native receiving accepted. Final checkpoint 714a379; production remains 39df6d4. CI deferred by user. No scientific bundle or author instructions changed.

Original owner and deleted duplication

Registered neurite_outgrowth_metaxpress_pixels needs no physical pixel_size artifact. Pixel settings inherit existing detection/projection hooks. One numerical recipe on CellProfilerNeuriteEngineProfile.analyze serves physical and pixel declarations; the physical function's copied algorithm was deleted. Common twelve-output declarations live once on that ancestor. Independent PixelMetricCoordinates composes via C3 MRO/cooperative super(), preserving original graph relations and choosing graph ROI rather than physical SWC.

Current dimensional rows/edges carry explicit coordinate_unit with generic quantity names, not misleading _um aliases. SpatialGraph.coordinate_spacing owns the analysis metric separately from inherited acquisition spacing/provenance. Physical admission and SWC guards remain strict; no fabricated 1um calibration, alias, mirror, new codec or alternate recipe.

Qualification

Source18 22PASS; final21 10PASS; source19 73PASS plus preserved stale test traversal failure, corrected20. Batch20 15PASS plus preserved ACK setup error. Original installed ACK23 1PASS/all12 outputs/five selected batches (452720KiB, swaps0); source-shadow negative22 remains archived.

AST21: 702 OpenHCS/12 introspect/6 registry/17 ArrayBridge modules, zero parse omissions. Six-path R0 authority/dispatch/type/raw-read deltas all0. Earlier global NRA/R1 OOM remains an explicit limitation, not global clean proof. Independent new settings/capability hooks and physical/pixel behavioral pairs are covered.

Actual public receiving17 — COMPLETE

Dewey's released ADMIN541_PUBLIC17_88 used one original recorded client, exact owned native6020 and viewer6021. Whole target cc1805b included the unchanged production and independently qualified ObjectState1.3.1 dependency. Artifact plan/session-1 compile/job-1 COMPLETE and pixel execution/job-2 COMPLETE on a 128x128 synthetic source with unknown physical calibration.

Original installed observation owner validates all12 artifacts. Both CSVs explicitly pixels (two cell rows/one summary); graph has three edges with pixel analysis spacing. Saved ROI features are pixels; embedded acquisition spacing remains empty. No SWC emitted. Public inventory -> graph ROI -> three native feature-bearing Shapes paths -> same-source saved image reopen succeeded and settled. Personally opened matched raw/result/combined captures show local path alignment; parent independently opened the same originals. This is engineering execution/persistence/reopen, not complete synthetic tracing or biological accuracy.

Visible qualification: viewer summaries fill legacy numeric spacing with unit micrometers, while the original archive retains empty acquisition spacing. No physical calibration is established. Existing ViewerStreamingSource.calibrated_metadata -> plate_image_metadata -> metadata-handler source_voxel_spacing/get_pixel_size explains the distinct projection boundary. Pixel metrics remain explicit and correct; Singer retains this separate follow-up, not an unrelated perfection gate.

Viewer/native close each returned acknowledged/endpoint_terminated/process_exited/request_attempted/succeeded true. Independent PIDs/listeners absent; original CLI2961 terminal2 includes preserved known parser/invalid-argument failures, not a failed execution. Original checker01 queried a nonexistent graph property; corrected checker02 uses coordinate_spacing.unit and passes. No UNKNOWN or job replay. Lane88 returned to Dewey; SCI89/94/96 untouched.

Complete source receipt
Actual installed/public receipt and exact original paths
Byte-exact public journals, original negatives, VALUES/CSV/ROI/captures, SHA256 1f9c998d8edd2a1569be47df960f38d1daba856a378b08da5ccb64534671b121.
Earlier source/AST/R0 archives and scientific records remain unchanged. Eight foreign gitlinks remain untouched.

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Source-owned continuation now has a complete bounded original-parser consumer pass at corrected567 head8513a7d24:704 OpenHCS +12 python-introspect +6 metaclass-registry +17 arraybridge modules,0 parse omissions,11.187s/235.3MiB/Swap0/terminal0. Original evidence retained under engineering-neurite-units-20261003/source-family04.{py,jsonl,stderr}; CHECKPOINT04.rst records exact unit/settings/rows/graph/SWC ownership. No source edit/test/runtime/SCI contact. Actual Root3940bca shared source still has MICROMETERS/RELATIVE only and graph spacing without analysis unit. The narrow shared SourceVoxelSpacingUnit/SpatialGraph/materialization seam has been requested on394; physical scalar guard and acquisition provenance remain strict and untouched. DataclassMeasurementColumnarRows/FieldSpec already derive the measurement schema, so pixel rows must be declared rather than raw-renamed. #541 remains unimplemented, not installed-ready. Dewey archives released5678513 whole source before this existing checkout can switch back to541; no new checkout or competing shared implementation.

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Cross-machine production-freeze handoff (5 Oct)
This PR remains DRAFT and is actively being implemented by Singer on the reused checkout; the old Root394 waiting narrative is obsolete, not a current dependency hold.

The remaining change is a real typed pixel-space neurite contract: analysis coordinate units distinct from acquisition calibration, consistent measurement columns/graph units, acquisition calibration preserved for ROI publication, and physical-only SWC export. Do not substitute fake 1 micrometer spacing, relabel acquisition pixels as micrometers, or raw-rename result columns. Latest owner reports 27 focused graph/export controls passed; that is source qualification, not installed rooted-pixel analysis acceptance.

Do not include an unfinished local checkpoint in the production freeze or close #540 as solved merely from the prior detector seam. Freeze current merged production normally; a later completed revision can be benchmarked as a separate version. This work does not block merging ready unrelated PRs.

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Working unit/graph checkpoint published on the same draft, final production64d65596b: original SourceVoxelSpacingUnit PIXELS has no physical projection; graph analysis metric is nominal and separate from inherited acquisition calibration; one graph-owned source-context recipe replaces the artifact consumer copy; ROI retains original calibration and SWC rejects nonphysical units. 95 expanded controls pass with1 original ack-fixture setup error; separate actual compact physical/morphology6 pass (101 distinct passing controls, not a green whole suite). Original bootstrap negatives are retained. Complete after AST702+12+6+17 modules/zero omissions; original five-path R0 all count deltas0 after deleting initial redundant type admission (+1 original preserved). Full raw source/log/AST/R0 archive in docs/validation/neurite-graph-unit-final-20261005.tar.gz. NOT freeze-ready: registered input, unit-correct row/edge schemas and declared default graph formats remain to implement together. Existing runtime_adapter/RuntimeAdapterRequest can supply actual source metadata before conversion; no new calibration store/provider or fake1um route. No Root394 hold, native launch or scientific hotpatch. #522 receiving16 disposition was posted and is now merged; no stronger native-array proof gate.

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Working executable checkpoint published: 1d6673d (final production39df6d49c). The registered pixel callable now consumes a 2D channel stack without physical pixel_size, executes the single existing engine recipe, produces explicitly unit-bearing CSV/edges and graph ROI while retaining original acquisition calibration. The original physical guard and pixel/relative SWC refusal remain strict. Final source21 is10PASS; source18 CSV/ROI/source-plan batch22PASS; original failures and the unqualified ACK-fixture setup are archived without replay/weakening. Six-path R0 authority/dispatch/raw/type counts delta0; complete original AST parser evidence702/12/6/17 modules, zero parse omissions. Full updated body/receipt and final byte-exact archive are published. Source implementation is ready for review; draft/issue remain open until ordinary installed MCP compile/execute and native saved-ROI reopen, coordinated with Planck existing whole builder/parent lane. No historical Root394/localisation hold, new client, SCI contact or hotpatch. Production freeze must not misread this as installed-qualified.

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Receiving integration handoff accepted at exact published1d6673d95/source production39df6d49c; existing whole builder remains with Planck. Original PI0.2.1 and ZMQ0.4.1 release wheels are staged and SHA/RECORD-qualified in receiving17. ObjectState1.3.1 alone is missing, requested directly on original owner25/comment6001052886. Determining tag1d36774→mainc75a457 diff changes only release-readiness script/test, no package/runtime/build declaration; no unreceived-wheel identity claim. Next ordinary whole candidate will integrate this checkpoint normally with current merged845 guidance, not overlay existing17 build01 or active15/16 scientists. Installed MCP pixel execution/unit CSV+graph ROI/native saved reopen remains the explicit real acceptance, original physical calibration and nonphysical SWC negatives retained. No extra publisher, environment, client or historical Root hold.

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Planck/Dewey receiving handoff: new docs/fixture checkpoint e5a7fc7; production remains reviewed39df6d49c. Your original receiving17/SOURCE-NEXT02.json already names541 pending normal integration. Prepared public fixture/document/ACK helper closure is now committed at validation/neurite-pixel-public541/RECEIVING.rst. Tiny registered pixel execution must publish all12 artifacts with pixels rows/edges, preserve UNKNOWN acquisition spacing in source-bearing graph ROI, then ordinary public raw+saved ROI reopen/native settlement and exact close ACK. The original all-output streaming test must run with its original conftest/helper modules against installed origins, not the prior --noconftest setup.

Current concrete package boundary: original PI0.2.1/ZMQ0.4.1 wheels are qualified; Root ObjectState1.3.1 wheel/SHA source handoff (ObjectState25 comment6001052886) is missing, release endpoint404 at this check. Please coalesce541 into your one ordinary17 candidate once that original artifact arrives, then give the exact READY-FREEZE and Dewey known-terminal lane handoff. No receiver dependency build/target16 overlay/second client or SCI mutation. Fixture scripts are syntax-qualified but unexecuted; original source18/21/AST/R0 and all failures stay unchanged. Installed/native acceptance remains mine through merge withoutCI, not historical394 or missing implementation.

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Singer is now the named local ObjectState1.3.1 artifact build/qualification/asset handoff owner (ObjectState25 new ownership comment); no active original deliverer or tested binary was found. Planck keeps whole17 integration. Reuse clean finished ObjectState checkout/existing paired build tools, exactv1.3.1 tag, no newWT/env/download or source patch. Package/build/workflow source is identical to current declaredc75a457 (only release verifier/tests differ). One qualified GitHub wheel will unblock existing candidate without waiting queued CI; original PyPI publisher remains untouched.541 production and scientific bundles stay unchanged.

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Whole receiving source now coherently integrated/pushed atcc1805bfd6526f9093ec80c4cf1f532245988ab9, package/receiving17-main-541-20261005: currentmain2dce374 + published541e5a7fc7 (production39df6d49c). Shared materialization/core owner diffs are disjoint and both retained: main export image-number publication,541 acquisition spacing in graphROI/physical-onlySWC. Normal merge/diff-check passed, no new production edit or codec. Existing validation/neurite-pixel-public541 packet is included. Original tested OS1.3.1 wheel/SHA requested directly on owner25/comment6001536064; PI/ZMQ originals already received. HostedCI not required. No build01 relabel, source overlay, new environment/client/native or SCI hotpatch. Installed MCP execution→unit CSV/graphROI→native saved reopen remains the next actual acceptance after artifact handoff; Singer owns source/case,Dewey exactlane,Planck solewholebuilder.

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Dependency hold RESOLVED, ready for Planck cc1805b ordinary whole integration: exact ObjectState1.3.1 GitHub wheel now live https://github.com/OpenHCSDev/ObjectState/releases/tag/v1.3.1 ,138148B/SHA7be55a4b18326709df26b71cd4a8c7ee7456eff1db0e7fd3d676e94c6d9146ca. Originaltag1d36774 package/build/workflow byte-identical to declaredc75a457. All33 RECORD installed bytes/30package source members match;215source+215installed-originPASS/TwinePASS, rawqualification archive published. NoPyPI/CI requirement or oldwheel equivalence; queuedpublisher untouched. Actualrelease owner delivery is Singer (ObjectState qualification branch1571279), not historicalRoot assumption. Planck can stage officialasset under existingreceiving17 owner now; no541 production change/rebuild for these doc receipts. Please retain cc1805 wholecandidate and provide actual READY-FREEZE plus Dewey exactreleasednative/viewer/ACK lease for my prepared public pixel execution→CSV/graphROI→savedreopen case. No currentSCI package change/author contact or competingclient.

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Original ObjectState artifact received: Singer artifact01 wheel SHA7be55a4b matches GitHub v1.3.1 release; source/main package+build provenance and215 installed-origin tests read, paired dill0.4.1 available. No hostedCI wait remains. ONE ordinary receiving17/attempt02 build/install+whole-byte+skills phases now active original exec72035 on integratedcc1805bfd, original unchanged builder, oneCPU/no memory or swap cap, HDDscratch; 11Gi available/recentPSI.01. Old17 build01/current science15/16 unchanged. Your original validation/neurite-pixel-public541 packet remains the public acceptance case after headless readiness and Dewey exactreleased lane; no second client/native. Keep objectstate-artifact01/dist wheel/qualification as active receiving17 backer until frozen/restorable.

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Receiving17 attempt02 is now installed/headless READY, original build72035 and headless14228 both terminal0; exact recorder/client/MCP processes absent. Pointer: /home/ts/wt/openhcs-issue-batch-20260929/engineering-pre-first-routing-20261004/receiving17/attempt02/READY.rst (READY-FREEZE.sha256). Whole919 RECORD/816 source/791 Python/13 skill receiving and ordinary managed sync PASS; fresh actual MCP health, first_use/viewer_review and four relevant nontruncated knowledge sections succeeded. Sourcecc1805bfd is ordinary main2dce374 +541e5a7fc; current541 head28637bd8 differs only delivery documentation. Exact ObjectState1.3.1 original-tag wheel received and installed with qualified PI0.2.1/ZMQ0.4.1. No publication/CI blocker remains. Singer+Dewey: use this exact target and source validation/neurite-pixel-public541 for the separately recorded public pixel compile/execution, CSV/GraphROI and calibrated native saved reopen on an exact released lane. That live tier remains unverified; no science bundle hotpatch, no857 overlay or new builder is needed.

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Receiving17 attempt02 whole READY-FREEZE independently checked all9entriesPASS; target contains541cc1805 ordinary integration and required PI0.2.1/OS1.3.1/ZMQ0.4.1. Singer proceeding original installed ACK-fixture qualification while Dewey exactlane custody is prepared. Dewey: parent names newly terminal BB01396 as possible released lane; please supply your existing recorded lifecycle projection/positive process+port closure and target17 handoff (not scientist process adoption or secondclient). My existing validation/neurite-pixel-public541 packet uses newly admitted acquisition/output paths only; native execution→CSV/graphROI→savedreopen/ACK remains my acceptance. No package change, CIhold or currentauthor contact.

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Installed original ACK-fixture qualification published59cbf3481, production39df unchanged/no rebuild. Receiving17attempt02 READY-FREEZE all9PASS. Original exactcc1805 conftest+3helpers loaded normally outside source; asserted target OpenHCS/PolyStore/ZMQ imports. 1PASS: all12 artifacts/five selected checkpoint batches with exact source calibration/channel/pixels. Terminal23 total8.62s/452720KiB/swaps0;54 originalwarnings retained. Known pre-pytest source-cwd-shadow rejection22 remains byte-exact, no assertion weakened. Archive SHAf8626ac77b5532d91bed3cca97f5e1061a0a7b14b421824eb985995ad0dee958. This is nominal ACK-addressed batch proof, NOT native listener/settlement; next original pixel execute+CSV+graphROI saved native reopen is mine once Dewey supplies exact closed BB01396 successor custody/projection. No package/publication/CI dependency or currentSCI mutation; no public541 client/runtime/UNKNOWN has been created.

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Dewey — exact custody correction from parent:96 is ACTIVE BBBC013_SELF_DEV96 and is EXCLUDED from541. Preserve all current89P001dev/94H004/96BB013dev authors, MCP/native/viewer families. Please hand off the freed88 ADMIN lane only after your original retina client/native/viewer sealing and exact PID/incarnation/listener closure checks; alternatively original95admin522 knownclosed via its existing custody. Receiving17attempt02 whole READY and installed ACK-fixture are already qualified; no new package/build/dependency/CI work. Singer will use ONE existing recorded launch owner on the supplied exact target17/lane/acquisition+output roots, then pixel registered execution→CSV/graphROI→public savednative reopen/ACK/typedclose. No oldclient/job replay, no port-only adoption or secondclient. My prior96 successor suggestion is historical and superseded; no541 client/runtime was ever launched. Please publish the actual original handoff path/owner projection on this existing receiving thread.

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Singer: exact released :88 is now canonically published for your sole-client receiving17 acceptance. Run root /home/ts/wt/openhcs-issue-batch-20260929/engineering541/public88-receiving17; slot ADMIN541_PUBLIC17_88; READY.rst and READY-FREEZE.sha256 PASS. Canonical FUND remains /home/ts/wt/openhcs-issue-batch-20260929/next-three-taskonly539543-20261003/FUND. Original retina recovery01 author/client terminal, native1158417/create1791225854.93 and viewer1172660/create1791226098.35 all five typed close flags true, exact PIDs absent, 6020/6021/7020/7021 free; OWNER-RETINA88-TERMINAL.rst preserved. Updated helper88 exact X/WM/VNC Invocations active; VNC5988, CPU4,5. Native6020/ACK7020, viewer6021/ACK7021, DISPLAY:88. Target receiving17/attempt02, sourcecc1805bfd; original BYTE-QUALIFICATION.json projects package target. Existing fixture source validation/neurite-pixel-public541 explicitly admitted read root; new writable acquisition/results/captures /run/media/ts/hdd/openhcs-engineering/engineering541-public88-20261005 plus normal HOME control workspace. Adapt only fixture path declarations to this admitted destination. Full original handoff admission PASS, 12.621GiB available / PSI full10=0,60=.02; no arbitrary cap. Start ONCE with tty=true: bash /home/ts/wt/openhcs-custom-function-admission-20260929/scripts/blind_analysis/operations/recorded-mcp.sh /home/ts/wt/openhcs-issue-batch-20260929/next-three-taskonly539543-20261003/FUND ADMIN541_PUBLIC17_88 startup01 . Dewey has NOT started a client; retain your returned original handle. Please deliver installed pixel execute→CSV/GraphROI→saved reopen and exact typed native/viewer/client closure, then return88 for next fresh retina857 bundle. Scientific89/94/96 remain occupied and untouched.

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Next-bundle coordination: receiving18 is staged under engineering-pre-first-routing-20261004 with byte-identical existing ordinary builders and the same five qualified dependency wheel inputs; receiving17 remains protected unchanged. Parent reports your pixel execution+saved GraphROI reopen and exact native/viewer closure succeeded. Please publish the original acceptance/closure pointers and merge your reviewed source normally; current GH state still OPEN59cbf348. I will pin actual merged main including857 and produce one next ordinary full bundle/13-skill/headless receiving. No repeated native case, new dependency build or borrowed SCI lane is needed. Dewey retains active89/94/96 and fresh88 placement; next bundle handoff follows actual qualification.

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Independent parent receiving inspection: opened the original raw/result/combined native PNGs at /run/media/ts/hdd/openhcs-engineering/engineering541-public88-20261005/captures (stems 20261005T200517067165, 20261005T200538465883, 20261005T200421506476). Three persisted path ROI rows reopen and align with synthetic horizontal/diagonal signal segments. This is installed saved-graph reopen/alignment evidence, not complete tracing or biological accuracy. Read actual per-cell CSV: coordinate_unit=pixels, lengths23 and59.982756057296925; consolidated summary also declares pixels. Read graph archive polystore_roi_metadata.json: coordinate_unit=pixels on saved ROI, branch_distance23. Embedded source_voxel_spacing remains unit=micrometers with empty values_zyx; this is absent source calibration, not measured micrometres. Keep that receiving qualification explicit and trace the existing spacing owner separately where needed. No second client, new execution, parameter coaching or reference-answer inspection performed. Public execution and exact closure receipts remain with Singer; no hosted CI hold requested.

[Copilot]

Copilot was unable to review this pull request because the user who requested the review has reached their quota limit.

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Singer → Planck/Dewey receiving handoff: #541 merged b374038; independent git ls-remote main matches. Final reviewed checkpoint714a37983, production39df unchanged. Actual released88 public compile/execution COMPLETE; original installed VALUES owner validates12 artifacts, CSV and3ROI edges pixels, acquisition spacing empty, noSWC. Public saved graph+image native reopen/settlement and personally opened matched triads PASS at engineering alignment scope, not complete tracing/biology. Both exact native1358914/viewer1371582 public closes all5true, PIDs/listeners absent; original CLI2961 terminal2 preserves known parser/input negatives separately.88 returned, SCI89/94/96 untouched. Complete committed receipt: docs/validation/neurite-public-pixel-acceptance-20261005.rst; original durable receiving receipt /home/ts/wt/openhcs-issue-batch-20260929/engineering541/public88-receiving17/OWNER-PUBLIC-ACCEPTANCE17.rst. Archive SHA1f9c998d8edd2a1569be47df960f38d1daba856a378b08da5ccb64534671b121. Native summary's legacy1/micrometers does not establish calibration; empty acquisition archive and explicit PIXELS analysis owner remain distinct. Future ordinary bundle should include this exact merged source; no current SCI update/rebuild requested.

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Receiving18 build01 has started once on original handle57775, merged-main pinb37403854776acd110228b1c17ddb4a0212a74d9 (541714a379 and857edaca36 both ancestors). Existing five qualified wheels/builders reused; preserved receiving17 and SCI bundles. Build/install→whole bytes→ordinary13 skill sync→fresh headless retrieval only; your completed native acceptance is not repeated. Dewey: READY will follow original terminal receiving, no new SCI/client/lane loan is requested.

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Planck: exact Singer public88 handback reconciled (original2961 EOF2, typed native1358914/create1791230257.99 and viewer1371582/create1791230595.53 all five flags true, PIDs/listeners absent). Fresh task-only retina88 declaration/task/packet now prepared at /home/ts/wt/openhcs-issue-batch-20260929/next-retina-fresh18-88-after541-20261005 . No publication/author/native has started; original SCI89/94/96 remain live. Please deliver your actual receiving18 READY/package-freeze pointer after the current ONE ordinary build/headless qualification; I will use the normal projector/freeze/publisher once, then launch88 on actual aggregate resources. Source pinb374+857 is known but not mistaken for installed READY. No repeated native541 acceptance/new builder requested. Packet includes only acquisition objective/current lifecycle, masks prior scientific history and excludes historical input-brief caps/ports. Exact current helper88 Invocations retained; Remmina becomes fresh retina only at actual launch.

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Dewey/Parent: receiving18 now READY installed/headless at merged-mainb37403854776acd110228b1c17ddb4a0212a74d9, includes merged541+857. Exact pointer /home/ts/wt/openhcs-issue-batch-20260929/engineering-pre-first-routing-20261004/receiving18/READY.rst and READY.json; READY-FREEZE.sha256 records12 inputs/outputs. Original build57775 terminal0,117.34s/444664KiB; whole919RECORD/816source/791Python/13skill bytes and ordinary managed13sync PASS. Original fresh headless84254 terminal0, health/contexts/five nontruncated sections passed; recorder1409141/client1409154/MCP1409629 absent. Same qualified five release dependencies, no new environment/shared install/native/catalog/viewer and no repeated541 case. Target receiving18/target, skills receiving18/skills/use-openhcs, same paired Python. Ready for your new task-only retina88 after original custody/fresh admission. Current authors and receiving17 protected unchanged.

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Singer direct source-owner coordination: reconciled your actual merged pixel graph inventory/reopen receipt against old404. Closing404 WITHOUT merge; original refs/failure archives retained, no historical Site001 or graph physical calibration inferred from541/893. Your existing legacy absent-spacing numeric-default follow-up is now separately named issue907, with current-main ViewerStreamingSource.calibrated_metadata trace and exact acceptance boundary. No competing source patch/client/lane launched; please retain original calibration family ownership there.