AGENTS.md

Agent operating contract

This repository processes scientific source data. Correctness and traceability are more important than throughput.

Non-negotiable rules

1. Do not write to raw images. Do not overwrite output outside the exact slide list requested by the user.
2. Run sppatch integrity before generating coordinates for a new collection. A slide with any strict decoding error is excluded until its source data is replaced or re-exported.
3. Never infer marker identities from a dye or filter name alone. Preserve the raw channel label unless an image-aligned metadata mapping is explicitly supplied.
4. Keep the generic foreground profile generic. A manual correction requires a named slide, documented QA evidence, normalized ROI coordinates and a reason. A rectangle is never automatic foreground.
5. Save/inspect QC artifacts before declaring a segmentation successful: thumbnail, binary mask, contour overlay, GeoJSON and coordinate count.
6. Prefer a small representative run before an entire dataset. Preserve successful outputs when retrying failed or manually corrected slides.

Required task sequence

Follow these cards in order:

1. harness/tasks/01-discovery.md
2. harness/tasks/02-integrity-and-baseline.md
3. harness/tasks/03-reviewed-corrections.md
4. harness/tasks/04-release-and-handoff.md

Definition of done

A run is complete only when the manifest, HDF5 output, channel/marker metadata, QC artifacts, integrity report and exception log agree on the same slide set. Do not describe an empty mask, decoder failure, unresolved channel names or an an undocumented special-case correction as successful.