chore: migrate pre-commit to prek with workspace mode

[einarwar]

Summary

Replaces the pre-commit framework with prek — a faster, drop-in compatible Rust reimplementation — and adopts prek's workspace mode to split the configuration into one config per project.

Why

• Version drift: ruff and biome were previously installed twice — once via the astral-sh/ruff-pre-commit / biomejs/pre-commit hook repos at one version, and again as dev dependencies in api/pyproject.toml / web/package.json at another version. Hooks now invoke the project-pinned binaries (uv run ruff, yarn biome), so the version in the lockfile is the version that runs.
• Speed: prek runs hooks in parallel where possible, has no Python bootstrap, and shares language toolchains across hooks.
• Monorepo ergonomics: with workspace mode, project-specific tooling lives next to the project it covers.

Layout

File	Scope
.pre-commit-config.yaml	Cross-cutting checks: commit message format, file parsers, whitespace/EOL hygiene, OpenAPI spec + API client build hooks.
api/.pre-commit-config.yaml	ruff check --fix + ruff format, run via uv run from api/.
web/.pre-commit-config.yaml	biome check --write, run via yarn biome from web/.

prek discovers all three configs automatically and runs hooks from the deepest project up — api and web first, then root.

Other changes

• .mise/config.toml: replace pre-commit = "4.5.1" with prek = "0.3.11".
• api/pyproject.toml: add ruff>=0.15.12 to the dev group so the pinned version drives both the editor and the hook.
• biome.json: enable vcs.useIgnoreFile so biome respects .gitignore (avoids linting the yarn-generated .pnp.cjs / .pnp.loader.mjs).
• .github/workflows/linting-and-checks.yaml: install api/web dependencies before running prek run --all-files, since the ruff and biome hooks shell out to uv / yarn.
• docs/docs/contribute/development-guide/01-setup.md, RUNBOOK.md: updated user-facing references to point at prek.

Validation

prek run --all-files and prek run --files <…> were exercised against representative files from each project to confirm scoping is correct:

Edited file	Hooks that run	Hooks that skip
api/src/app/features/.../*.py	ruff, ruff-format, generate-openapi-spec, root checks	biome, generate-api-client-from-spec
api/tests/conftest.py	ruff, ruff-format, root .py parser	generate-openapi-spec (outside trigger pattern)
web/src/App.tsx	biome, root whitespace/EOL	ruff, openapi hooks
web/package.json	biome, check-json, whitespace	ruff, openapi hooks
api/.openapi.json	generate-api-client-from-spec, check-json	ruff, generate-openapi-spec
README.md	only root whitespace/EOL/line-ending hooks	everything else

Migration for contributors

Install prek (any of: mise install, uv tool install prek, pip install prek, brew install prek) and run prek install once to register the git hooks. The project's .pre-commit-config.yaml files work unchanged with the legacy pre-commit CLI as well, so no flag day required.

[Copilot]

Pull request overview

This PR migrates the repo’s git hook runner from pre-commit to prek and adopts prek “workspace mode” so project-specific hooks live under api/ and web/, while the root config retains cross-cutting checks and build hooks.

Changes:

• Replace ruff/biome hook repos with local hooks that shell out to project-pinned binaries (uv run ruff, yarn biome) via workspace-scoped configs.
• Update CI to install API/Web dependencies before running prek run --all-files.
• Update developer docs/runbook references and enable Biome’s vcs.useIgnoreFile to respect .gitignore.

Reviewed changes

Copilot reviewed 9 out of 10 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
.pre-commit-config.yaml	Converts root hooks to workspace-mode-friendly layout; removes ruff/biome hook repos.
api/.pre-commit-config.yaml	Adds API-local ruff hooks executed via uv run.
web/.pre-commit-config.yaml	Adds Web-local Biome hook executed via yarn biome.
.github/workflows/linting-and-checks.yaml	Switches CI from pre-commit action to running prek after installing deps.
.mise/config.toml	Replaces pre-commit tool pin with prek.
api/pyproject.toml	Adds ruff to dev dependency group to pin hook/editor version.
api/uv.lock	Locks ruff dependency in the API environment.
biome.json	Enables Biome VCS integration to respect .gitignore.
docs/docs/contribute/development-guide/01-setup.md	Updates contributor setup docs to use prek.
RUNBOOK.md	Updates runbook resource link to point at prek.

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