chore: update JavaScript and Python dependencies

[bigint]

Summary

Refresh JavaScript and Python dependencies so lockfiles and version floors track current library releases, and drop stale pnpm age-gate excludes that are no longer needed.

Changes

• Bump pnpm to 10.34.5 and update app, website, and TypeScript SDK packages (TypeScript 7, Vite 8.2, Next 16.3, Biome 2.5).
• Raise API Python floors and lockfile versions (Docling 2.124, FastAPI 0.141, Cohere 7.1, Pydantic 2.13, cryptography 50, redis 8, structlog 26, Ruff 0.16).
• Upgrade GitHub Actions (checkout@v7, setup-uv@v10, setup-node@v7, pnpm/action-setup@v6, build-push-action@v7).
• Switch Biome to preset: "recommended" and document JS/Python upgrade commands.

Related issues

N/A

Verification plan

• pnpm lint passes
• cd api && uv run ruff check . && uv run ruff format --check . passes
• Relevant typecheck, build, and runtime smoke checks completed
• Docs updated (website/content/docs/) if user-facing behavior changed

Notes for reviewers

OpenAI Python 3.x and MCP 2.x were left on current majors. A few npm packages newer than 7 days were skipped by minimumReleaseAge. tsr generate prints a replaceRouteChunk circular-dependency warning; the app still typechecks and builds.

Greptile Summary

The PR refreshes JavaScript and Python dependencies, updates CI and publication actions, regenerates the application route tree, and updates dependency-maintenance documentation.

• Raises dependency floors and regenerates the pnpm and uv lockfiles.
• Updates GitHub Actions used by CI and release workflows.
• Removes obsolete pnpm release-age exceptions.
• Adopts Biome’s recommended preset and documents JavaScript and Python upgrade commands.

Confidence Score: 5/5

The PR appears safe to merge.

No blocking failure remains.

Important Files Changed

Filename	Overview
api/pyproject.toml	Raises backend dependency floors across the API, ingestion, persistence, provider, and queue stacks.
pnpm-lock.yaml	Regenerates workspace resolutions for the updated application, website, SDK, and tooling dependencies.
api/uv.lock	Regenerates the API environment for the raised Python dependency floors.
app/src/routeTree.gen.ts	Regenerates the TanStack route tree with ordering-only changes and no identified route-semantic differences.
.github/workflows/ci.yml	Updates checkout and uv setup actions while preserving existing CI jobs and quality gates.
.github/workflows/docker-publish.yml	Updates checkout, QEMU, and Docker build actions without changing publication inputs or image identities.
biome.jsonc	Migrates the recommended-rule configuration to Biome’s preset syntax.
website/content/docs/development/dependencies.mdx	Expands dependency-maintenance guidance to cover both pnpm and uv workflows.

_{Reviews (2): Last reviewed commit: "fix: pin setup-uv to v10.0.1 so Actions ..." | Re-trigger Greptile}

[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-09-03T07:34:09.524274Z	2e7b07b	Draft marked ready

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