[trissim]

Summary

This recovers the useful uncommitted work that had accumulated on the stale pre-0.8.6 checkout and reapplies it to current main/v0.8.6 as reviewable commits.

• update ObjectState to reconcile historical snapshots against the current declared schema
• preserve exact source projections, persisted source metadata, and routed component coordinates through viewer streaming and validation
• derive viewer component domains from current route ownership and retain scalar-axis semantics
• make UI-bridge/MCP timeout and progress behavior explicit and typed
• strengthen round-object and neurite ownership analysis, including source-identifiable QA checkpoints and actionable agent guidance
• retain a reproducible blind-neurite preparation utility and matched-batch pilot driver/receipts
• revise the SLAS manuscript evidence, current-source neurite replay documentation, and generated figures

Architecture

The recovery keeps declarations as the semantic owners:

• exact viewer coordinates are emitted by the viewer state owner rather than reconstructed from payload summaries
• route-local component domains own values; shared domains are derived views
• projected artifacts carry typed source/group lineage instead of manufactured single-source context
• the catalog help repair lives on the public function declaration
• historical ObjectState values are projected onto the current construction schema; removed fields are discarded and new fields retain current defaults

Dependency

The first commit advances external/ObjectState to OpenHCSDev/ObjectState#7:

• Reconcile historical snapshots with current schemas ObjectState#7

That PR must merge before or with this one so the recorded submodule commit remains reachable from the canonical ObjectState repository.

Validation

• 1118 passed — every changed OpenHCS unit/integration test
• 205 passed — ObjectState suite
• 8 passed — shared paper-build/regression suite
• Ruff syntax/error selectors passed for every changed Python file
• Black 26.5.1 passed for every changed Python file
• broad tests/unit tests/core run reached 7406 passed; 47 of its 48 failures were caused by formatting source while the run was live and all 47 passed on a frozen-source rerun; the remaining catalog-help failure was repaired at the function declaration and passed independently

Intentionally excluded local artifacts

The recovery point remains preserved on wip/recent-unmerged-snapshot-20260917 at 7627c99bb.

The PR deliberately excludes generated/heavy local artifacts:

• benchmark/results/matched_batch_pilot_20260915/candidate_warmup/
• benchmark/results/matched_batch_pilot_20260915/native_warmup/
• benchmark/results/matched_batch_pilot_20260915/events_-1.json.gz
• root and ObjectState-local untracked uv.lock files

The small reproduction driver, design, README, environment/result summaries, and digest receipt are retained in Git; the paired microscopy outputs and raw event stream are not.