feat(mcp): read_paper folds annotations by default (#185 PR1/5)#186
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feat(mcp): read_paper folds annotations by default (#185 PR1/5)#186
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`read_paper` now returns a JSON envelope with paper, annotations[], source_version, extractor, path, truncated, total_chars. An agent calling the natural extraction endpoint will no longer silently miss human comments — closing one of the three legs of #185 (agent↔human comment loop). Pass `with_annotations: false` for the legacy text shape so existing clients can opt out. `get_annotated_paper` is documented as superseded by `read_paper` for fetches that also need the extracted body. Refs #185. [tape-exempt: MCP-only tool surface change; no TUI/CLI source touched]
Review nits on the prior commit: - assemble_read_paper_response now takes &Paper instead of paper_id + paper_title, dropping the second paper_repo.get on the with_annotations path. read_paper_tool already loaded the paper for the extraction cache check. - New `read_paper_with_annotations_replies_carry_root_id` test mirrors the existing get_annotated_paper test so future refactors of build_annotations_json don't silently break parent_id/root_id propagation through the read_paper envelope. Refs #185. [tape-exempt: MCP-only refactor + test, no TUI/CLI surface touched]
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Summary
First of 5 PRs landing #185 (agent↔human comment-and-reply loop). Closes the silent-miss bug where an agent calling the natural extraction tool (
read_paper) would never observe a human comment.read_papernow Returns: JSON{paper, annotations[] (live, with parent_id/root_id and full anchor), source_version, extractor, path, truncated, total_chars}by defaultwith_annotations: falsepreserves the legacy text shape byte-identically (escape hatch for any existing client)get_annotated_paperis documented as superseded byread_paperfor fetches that also need the bodybuild_annotations_jsonhelper so both tools agree on shapeTest plan
cargo test -p scitadel-mcp --libpasscargo clippy -p scitadel-mcp --tests -- -D warningscleancargo fmt --checkclean[tape-exempt: MCP-only tool surface change; no TUI/CLI source touched]
Refs #185.