Papergraph MCP

Findings (7)

• highHigh. Something risky that needs a close look before you install.
  dependencies issue

  Details are available to the maintainer after claiming this listing.
• highHigh. Something risky that needs a close look before you install.
  dependencies issue

  Details are available to the maintainer after claiming this listing.
• mediumMedium. Worth checking, often a vulnerable dependency or a setup problem.
  mcp@2.1.1: 4 known vulnerabilities

  GHSA-5h93-6whr-6q8j, GHSA-84m7-p3x7-pcfv, GHSA-rwrf-2pqf-9j8j, GHSA-w4fh-qvv9-3v23

  uv.lock
• lowLow. Minor, or common in normal tools. Shown for information.
  Possible example credential in docs/tests: generic-api-key

  4 matches in this file

  docs/examples/reference-search-example.json:47
• lowLow. Minor, or common in normal tools. Shown for information.
  Possible example credential in docs/tests: generic-api-key

  15 matches in this file

  docs/examples/reference-expansion-example.json:51
• lowLow. Minor, or common in normal tools. Shown for information.
  opentelemetry-api@1.44.0: 1 known vulnerability

  GHSA-xcq7-p3pf-p88h

  uv.lock
• lowLow. Minor, or common in normal tools. Shown for information.
  No manifest declaring network access and environment variables (agent.json)

Network activity

Tools exposed (68)

• get_environment_diagnostics

  Return PaperGraph version and reproducible launch diagnostics.

• validate_arxiv_input

  Normalize arXiv ID and URL inputs and return the safe next action.

• validate_arxiv_request

  Validate a raw user arXiv request and return the safe next action.

• open_workspace

  Open or initialize a persistent multi-paper workspace.

• workspace_add_local_paper

  Add or replace a local LaTeX project in the active workspace.

• workspace_add_arxiv_paper

  Add or replace an arXiv LaTeX project in the active workspace.

• workspace_add_pdf_paper

  Add or replace a born-digital PDF paper in the active workspace.

• discover_doi_paper

  Find exact DOI metadata and public body candidates; never download links.

• workspace_import_doi_candidate

  Import a selected root DOI PDF only after explicit review/confirmation. This is not permission to download newly discovered external references. Candidate provider identity is evidence, not a verification of PDF contents.

• workspace_add_doi_paper

  Load a user-requested root DOI when one public PDF candidate is eligible. Multiple candidates require user selection. Do not use for newly discovered external references: those require an import plan and review first.

• workspace_list_papers

  List all papers stored in the active workspace.

• workspace_get_paper

  Return metadata and counts for one stored paper.

• workspace_search_theorems

  Search theorem titles and bodies across the active workspace.

• workspace_get_dependencies

  Return dependencies of a globally identified stored theorem.

• workspace_get_dependency_diagnostics

  Explain how workspace dependencies were extracted for one theorem.

• workspace_get_citations

  Return incoming or outgoing citation evidence for a stored paper.

• workspace_list_results

  List a stable result page (limit 1..100). Advance offset by returned count. A full page may be truncated; continue until a page has fewer than limit results. This is not an unbounded complete list.

• workspace_get_result

  Return one stored evidence result with source spans.

• workspace_get_result_proof

  Return proof evidence for one stored evidence result.

• workspace_get_proof_dependencies

  Return proof dependency evidence for one stored evidence result.

• workspace_get_external_result_mentions

  Return external result mentions from a result's proof evidence.

• workspace_get_evidence

  Return metadata and source spans for one evidence node or edge.

• workspace_export_reading_bundle

  Export a paper-level evidence bundle for paper-reading consumers.

• workspace_export_result_reading_context

  Export focused evidence context for reading one result's proof.

• workspace_get_source_slice

  Return bounded source text around one span, result, or proof.

• workspace_read_source_blocks

  Read raw source blocks from a slice locator; follow next until null. Blocks are source text, with no inferred proof ownership. Works for legacy imports without changing reading data. A changed extraction needs new locators.

• workspace_get_result_reading_path

  Return deterministic local reading paths for one result.

• workspace_get_dependency_reading

  List main-result candidates or read a user-selected target with evidence. Statement references and proof-local dependencies remain separate. External references produce reviewable plans only; empty evidence is not independence.

• workspace_create_reading_session

  Create a persistent reading session in the active workspace.

• workspace_list_reading_sessions

  List persistent reading sessions in the active workspace.

• workspace_get_reading_session

  Return one persistent reading session with checkpoints and notes.

• workspace_record_reading_checkpoint

  Create or update a reading checkpoint in the active workspace.

• workspace_add_reading_note

  Add a note or question to a reading session.

• workspace_export_reading_session_summary

  Export a deterministic recovery summary for a reading session.

• workspace_create_reading_queue

  Create a persistent reading queue for one stored result.

• workspace_list_reading_queues

  List persistent reading queues in the active workspace.

• workspace_get_reading_queue

  Return one persistent reading queue with ordered items.

• workspace_apply_reading_queue_to_session

  Apply reading queue items as checkpoints in a reading session.

• workspace_plan_external_imports_for_result

  Plan external arXiv imports for one result's reading path.

• workspace_plan_external_imports_for_queue

  Plan external arXiv imports referenced by one reading queue.

• workspace_plan_external_imports_for_paper

  Plan external arXiv imports visible in one stored paper.

• workspace_resolve_external_reference

  Resolve a blocked external reference to a user-confirmed target.

• workspace_list_external_reference_resolutions

  List recorded external reference resolutions and selection provenance.

• workspace_search_external_reference

  Search scholarly metadata providers for a blocked external reference.

• workspace_list_external_reference_searches

  List scholarly reference search runs and candidates.

• workspace_resolve_external_reference_candidate

  Apply a searched candidate as an explicit reference resolution.

• workspace_get_paper_map

  Return an evidence-first first-load map for one stored paper.

• workspace_export_paper_reading_report

  Export a deterministic Markdown reading report for one stored paper.

• workspace_export_cross_paper_reading_plan

  Export a deterministic Markdown reading plan for selected papers.

• workspace_plan_starter_project

  Plan a Workspace Starter run without writing files.

• workspace_bootstrap_reading_project

  Create starter artifacts for a first reading project.

• load_paper

  Load a local LaTeX paper and build its theorem graph.

• load_arxiv_paper

  Download an arXiv source project and build its theorem graph.

• load_arxiv_request

  Validate a raw arXiv request, then load it only if unambiguous.

• list_theorems

  List theorem-like environments in the currently loaded paper.

• get_theorem

  Return the full text and metadata for one theorem-like node.

• get_dependencies

  Return theorem-like nodes referenced by the given theorem.

• get_dependency_diagnostics

  Explain how dependencies were extracted for one theorem-like node.

• where_used

  Return theorem-like nodes that reference the given theorem.

• workspace_create_reference_expansion

  Save an approved finite expansion policy. Creation does not search or import.

• workspace_advance_reference_expansion

  Execute the saved policy: search, download arXiv sources, import unique strong candidates and record resolutions without per-paper prompts, within approved budgets. Resume with the same run ID.

• workspace_get_reference_expansion

  Read saved graph, counts, decisions and continuation actions without network.

• workspace_list_reference_expansions

  List saved expansion summaries, optionally filtered by state.

• workspace_decide_reference_expansion

  Record exactly one candidate_id, target, existing_paper_id, skip:true or retry:true. Advance separately to execute the approved choice.

• workspace_update_reference_expansion_policy

  Explicitly revise numeric budgets; cumulative usage is retained.

• workspace_pause_reference_expansion

  Pause scheduling after the active step. Advance explicitly to resume.

• workspace_cancel_reference_expansion

  Permanently stop this run, preserving imported papers and history.

• workspace_export_reference_expansion

  Return saved JSON or Markdown without writing client files or using network.