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alexmandClaude 7890fa1ad7 feat: trace annotation body for traced citations; paperspec.traces
A trace follows one citation of a sentence of a citing paper to a passage of the
cited paper (spec/18 section 18.5). Minor change: a new body kind, optional
properties and two rules, with no valid file made invalid.

- annotation schema branch (source, selector, reference, note, verdict, proposer;
  proposer required for a Software creator); body_kind in sql/store.sql; the note
  and proposer terms of the JSON-LD context; rules layer.trace.source and
  layer.trace.target.
- paperspec.traces: resolve(annotation, citing_state, cited_state, same_as) gives
  current, changed, stale, unlinked or misresolved with open and cites; problems,
  disputes, disputed.
- fixtures/records/traces/ on writer2027fixed-ynr7.v3 and vectors/traces.jsonl
  (29 cases); check.py runs the record checks over both layers; counts, glossary,
  examples and CHANGELOG updated.

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01Uy4ZYbWRoCdUtWLEfigysY
2026-10-17 20:12:04 -04:00

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{"claims":{"paperclaim":"amber"},"datasets":["ds-hale-bond-params","ds-hale-ctct-scan"],"documents":[{"doc":"smithlab/hale2026harmonic-damb","reason":"The bond constants we start from.","status":{"Ben Example":"read","Cara Example":"reading"},"tags":["parameters"]},{"doc":"okafor2025solvent-acth","reason":"Solvent shifts for the validation set.","tags":["spectra"]}],"drafts":["smithlab/writer2027fixed-ynr7.v3"],"format":"scienting-project/1","key":"smithlab-charges","layers":["tag:scient.ing,2026:layer:smithlab/kp4m2x7q","tag:scient.ing,2026:layer:smithlab/tr6c3q8m"],"members":[{"keys":["ana"],"person":"Ana Example","role":"owner"},{"keys":["ben","ben-spot"],"person":"Ben Example","role":"editor"},{"keys":["cara"],"person":"Cara Example","role":"reader"}],"name":"Charges and bonds","paths":[{"id":"onboarding","steps":[{"note":"Read the introduction.","ref":"smithlab/hale2026harmonic-damb","type":"document"},{"note":"Then the table.","ref":"smithlab/hale2026harmonic-damb#hj4s7pb","type":"node"},{"note":"The bond force constant, amber/k-bond.","ref":"claim:272XTX7C","type":"claim"}],"title":"First week"}],"settings":{"digit_rule":"anchored-sections","drift_threshold":"0.25","log":{"origin":"scient.ing/log/smithlab","threshold":1,"witnesses":["wit"]},"rights_unknown":"refuse","spot_check":{"minimum":10,"rate":"0.05"},"stages":"scienting-stages-default"},"store":"smithlab","views":["ctct-scan"]}