Claude Code entrypoint only: - Use AGENTS.md for shared repository instructions. - Keep Claude-specific additions here short and tool-specific. - Prefer make ci-local before final handoff (runs lint-loc, the 600-LOC budget). - FastMCP 3.x symbols are post-training-cutoff and fast-moving — verify imports against the installed package before relying on them (see the import smoke in docs/plans/2026-06-13-genefoundry-router-implementation.md, Task 2). - When a backend's source repo adopts Tool-Naming Standard v1, delete its transform block from servers.yaml rather than adding router-side workarounds.
This file orients Claude Code (and other agents) in this repository. Read AGENTS.md first — it is the authoritative contributor and agent guide (architecture, invariants, conventions, definition of done). This file only highlights the essentials. hpo-link is an MCP + REST server over the Human Phenotype Ontology (HPO), backed by a locally-built SQLite database. It serves phenotype term lookup, is_a hierarchy traversal, cross-ontology mapping, and gene↔phenotype↔disease association queries (HPOA). It mirrors the sibling mgi-link stack. See AGENTS.md for the full…
Read AGENTS.md first — it holds the engineering conventions and architecture invariants for this project. mgi-link is an MCP server grounding mouse-genetics work in MGI (Mouse Genome Informatics). It reproduces…
Claude Code entrypoint only: - Use AGENTS.md for shared repository instructions. - Keep Claude-specific additions here short and tool-specific. - Prefer make ci-local before final handoff. It runs lint-loc, which enforces the 600-LOC per-file budget. - When planning an edit that would push a stringdb_link/ module past ~500 lines, propose a split first rather than growing the file. - When a split is required, prefer cohesive sub-modules under a package directory; keep existing public facades stable so call sites do…
Claude Code entrypoint: - Use AGENTS.md for shared, repo-wide instructions (project areas, the snapshot/refresh workflow, coding standards, File Size Discipline). - make ci-local is the gate — run it before final handoff. - Use uv only; never pip install. Prefer Makefile targets. - Do not hand-edit the snapshot bundle (clingen_link/data/clingen.sqlite.zst) or tests/fixtures/.
Claude Code entrypoint only: - Use AGENTS.md for shared repository instructions. - Keep Claude-specific additions here short and tool-specific. - Prefer make ci-local before final handoff. It runs lint-loc, which enforces the 600-LOC per-file budget. - When planning an edit that would push a gnomad_link/ module past about 500 lines, propose a cohesive split first rather than growing the file.
This file guides Claude Code when working in this repository. Read AGENTS.md first — it holds the engineering conventions, architecture invariants, and the definition of done. They apply in full…
This file orients Claude Code (and other agents) in this repository. Read AGENTS.md first — it is the authoritative contributor and agent guide (architecture, invariants, conventions, definition of done). This file only highlights the essentials. - mondo-link is an MCP + REST server over the Mondo Disease Ontology, backed by a locally-built SQLite index. It mirrors the sibling mgi-link stack. - Two planes: the data plane (config/constants/identifiers/ingest/ data/services) builds & reads the index and returns plain dicts; the MCP plane…
Claude Code entrypoint only: - Use AGENTS.md for shared repository instructions. - Keep Claude-specific additions here short and tool-specific. - Prefer make ci-local before final handoff. It runs lint-loc, which enforces the 600-LOC per-file budget. - When planning an edit that would push a spliceailookup_link/ module past about 500 lines, propose a cohesive split first rather than growing the file. - Remember: the upstream scoring API reports errors as HTTP 200 + an error field, and calls can take 30s+.…
Claude Code entrypoint only: - Use AGENTS.md for shared repository instructions. - Keep Claude-specific additions here short and tool-specific. - Prefer make ci-local before final handoff. It runs lint-loc, which enforces the 600-LOC per-file budget. - When planning an edit that would push a vep_link/ module past about 500 lines, propose a cohesive split first rather than growing the file. - All Ensembl calls in tests are mocked with respx; never let a test reach the live network (the tests/conftest.py…
A file Claude Code reads at the start of every session. It holds the commands, conventions and warnings the agent needs for this project.
Where does it go?
At the repository root. Claude Code also reads CLAUDE.md files in subdirectories when it works there.
What should it contain?
Build and test commands, the project's layout, conventions that aren't obvious from the code, and mistakes to avoid. Short files tend to work better than long ones.
CLAUDE.md or AGENTS.md?
Claude Code reads CLAUDE.md; most other agents read AGENTS.md. Many projects keep one and point the other at it.
berntpoppCLAUDE.md