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Harden dependency baseline: upgrade axios/ws and enforce patched versions via pnpm overrides - #4

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sjoerd2025 merged 6 commits into
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copilot/implement-mcp-server-cloudflare-setup
Aug 1, 2026
Merged

Harden dependency baseline: upgrade axios/ws and enforce patched versions via pnpm overrides#4
sjoerd2025 merged 6 commits into
mainfrom
copilot/implement-mcp-server-cloudflare-setup

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Copilot AI commented Aug 1, 2026

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This updates the monorepo’s vulnerable HTTP/WebSocket client dependencies to patched releases and prevents transitive drift back to affected ranges. The goal is to keep installs/builds unchanged while closing known advisories in axios and ws.

  • Dependency security baseline

    • Upgraded direct deps in root package.json:
      • axios1.18.0
      • ws8.21.0
  • Transitive enforcement

    • Added root pnpm.overrides entries for:
      • axios: 1.18.0
      • ws: 8.21.0
    • Ensures workspace/transitive resolution does not reintroduce vulnerable versions.
  • Lockfile alignment

    • Regenerated pnpm-lock.yaml to apply and persist the new resolution graph.
{
  "dependencies": {
    "axios": "1.18.0",
    "ws": "8.21.0"
  },
  "pnpm": {
    "overrides": {
      "axios": "1.18.0",
      "ws": "8.21.0"
    }
  }
}

Summary by Sourcery

Upgrade and pin key dependencies, centralize tooling configuration, and refresh project setup and docs for a pnpm/Turbo-based monorepo workflow.

New Features:

  • Add repo-level SETUP.md documenting pnpm/Turbo workflows, prerequisites, and common commands.

Bug Fixes:

  • Adjust test helper ExecutionContext casting in mcp-common to avoid type issues with stateless MCP transport tests.

Enhancements:

  • Update axios and ws to patched versions and enforce their resolutions via pnpm overrides to strengthen the dependency security baseline.
  • Refresh core build and tooling dependencies (TypeScript, Vite, Vitest, esbuild, Prettier plugins, Cloudflare worker types) and align peer dependency rules and overrides across the monorepo.
  • Switch root scripts to use pnpm and Turbo for formatting, linting, type checking, and testing, standardizing CI/dev workflows.
  • Centralize linting and formatting configuration at the repo root (oxlint, Prettier) and remove per-app ESLint configs and legacy Prettier config files.
  • Add Vitest as a dev dependency in sandbox-container and eval-tools packages to align test tooling across workspaces.

Documentation:

  • Tidy README formatting for the Unified server entry and add setup/troubleshooting guidance for local development and deployment.

Tests:

  • Ensure Vitest-based test tooling is consistently declared in relevant packages and captured in overrides to stabilize test runs.

Chores:

  • Regenerate pnpm-lock.yaml, update turbo and wrangler configs, and adjust npm/pnpm configuration files to match the new dependency and tooling setup.

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changeset-bot Bot commented Aug 1, 2026

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⚠️ No Changeset found

Latest commit: 814e25b

Merging this PR will not cause a version bump for any packages. If these changes should not result in a new version, you're good to go. If these changes should result in a version bump, you need to add a changeset.

This PR includes no changesets

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Comment thread package.json
Comment thread package.json Outdated
Comment thread .prettierignore
Comment thread package.json Outdated
@sjoerd2025

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@copilot resolve the merge conflicts in this pull request

Copilot AI changed the title [WIP] Implement production-ready setup for mcp-server-cloudflare Harden dependency baseline: upgrade axios/ws and enforce patched versions via pnpm overrides Aug 1, 2026
Copilot AI requested a review from sjoerd2025 August 1, 2026 07:50

Copilot AI commented Aug 1, 2026

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@copilot resolve the merge conflicts in this pull request

Resolved. I merged origin/main into this branch and fixed the package.json conflict; the update is in commit a98335a.

Comment thread turbo.json
@sjoerd2025
sjoerd2025 marked this pull request as ready for review August 1, 2026 07:55
Copilot AI review requested due to automatic review settings August 1, 2026 07:55
@sjoerd2025

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@copilot resolve the merge conflicts in this pull request

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Caution

The consumer version of Gemini Code Assist on GitHub has been sunset. All code review activity has officially ceased.

@sourcery-ai

sourcery-ai Bot commented Aug 1, 2026

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Reviewer's Guide

This PR hardens the monorepo’s dependency and tooling baseline: it upgrades axios/ws to patched versions, enforces their resolutions via pnpm overrides, aligns the lockfile and root tooling with pnpm/Turbo workflows, and centralizes formatting/linting/configuration across the repo while adding setup docs.

Flow diagram for dependency resolution with pnpm overrides

flowchart TD
  A[pnpm install] --> B[Read root package.json dependencies]
  B --> C[Read pnpm.overrides]
  C --> D{Dependency is axios or ws?}
  D -->|yes| E[Force version axios 1.18.0 / ws 8.21.0]
  D -->|no| F[Resolve version from dependency tree]
  E --> G[Write resolutions to pnpm-lock.yaml]
  F --> G[Write resolutions to pnpm-lock.yaml]
  G --> H[Install dependencies across workspaces]
Loading

File-Level Changes

Change Details Files
Upgrade HTTP/WebSocket clients to patched versions and enforce them via pnpm overrides.
  • Bump root axios dependency from 1.8.2 to 1.18.0.
  • Replace ws ^8.18.1 with pinned ws 8.21.0 in root dependencies.
  • Add pnpm.overrides for axios and ws to force patched versions across all workspaces.
  • Regenerate pnpm-lock.yaml to reflect the new resolution graph.
package.json
pnpm-lock.yaml
Align root scripts and tooling with pnpm/Turbo-based workflows and centralized lint/format/test/typecheck.
  • Change the root check script to call pnpm-run sub-scripts instead of npm.
  • Switch format/format:check from oxfmt to prettier for repository-wide formatting.
  • Update lint/test/typecheck scripts to run Turbo pipelines (run-turbo) instead of direct tools.
  • Adjust vitest, vite, typescript, esbuild, prettier plugins, and related devDependencies to the new pinned versions used by the monorepo.
  • Add vitest as a devDependency in sandbox-container and eval-tools packages to match the root testing baseline.
  • Update turbo.json and wrangler.jsonc as part of the pipeline alignment.
package.json
apps/sandbox-container/package.json
packages/eval-tools/package.json
turbo.json
wrangler.jsonc
Centralize and tighten repo-wide configuration for peers, overrides, linting, and formatting.
  • Add pnpm.peerDependencyRules.allowedVersions in the root package.json to constrain allowed peer versions for key packages.
  • Extend pnpm.overrides to pin additional shared tools (typescript, vite, esbuild, vitest, @cloudflare/workers-types, oxfmt, oxlint, tsx, @types/node).
  • Introduce a new root .oxlintrc.json and .prettierrc.json to centralize lint/format config.
  • Remove per-app .eslintrc.cjs configs in apps and packages to rely on centralized tooling.
  • Update .npmrc, .prettierignore, and run-eslint-workers to be compatible with the new lint/format setup.
package.json
.oxlintrc.json
.prettierrc.json
.npmrc
.prettierignore
packages/tools/bin/run-eslint-workers
apps/ai-gateway/.eslintrc.cjs
apps/auditlogs/.eslintrc.cjs
apps/autorag/.eslintrc.cjs
apps/browser-rendering/.eslintrc.cjs
apps/cloudflare-blog/.eslintrc.cjs
apps/cloudflare-one-casb/.eslintrc.cjs
apps/demo-day/.eslintrc.cjs
apps/dex-analysis/.eslintrc.cjs
apps/dns-analytics/.eslintrc.cjs
apps/docs-ai-search/.eslintrc.cjs
apps/graphql/.eslintrc.cjs
apps/logpush/.eslintrc.cjs
apps/radar/.eslintrc.cjs
apps/sandbox-container/.eslintrc.cjs
apps/stack-mcp/.eslintrc.cjs
apps/workers-bindings/.eslintrc.cjs
apps/workers-builds/.eslintrc.cjs
apps/workers-observability/.eslintrc.cjs
packages/mcp-common/.eslintrc.cjs
packages/tools/.eslintrc.cjs
Minor code and docs adjustments to keep tests and documentation in sync with the new baseline.
  • Adjust a test helper cast in stateless-app.ts to use an intermediate unknown cast for ExecutionContext.
  • Tighten README table alignment for the Unified server row.
  • Add a new SETUP.md documenting prerequisites, pnpm/Turbo commands, workspace-level script patterns, and troubleshooting steps.
packages/mcp-common/src/test/stateless-app.ts
README.md
SETUP.md

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@sourcery-ai sourcery-ai Bot left a comment

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Hey - I've found 1 issue, and left some high level feedback:

Fixed security issues:

  • sharp (link)

  • undici (link)

  • ws (link)

  • The change from local .eslintrc.cjs files to a centralized .oxlintrc.json may drop app-specific lint rules or ignores; consider validating whether any app relied on custom overrides and, if so, recreating them via per-package config or root-level patterns.

  • The new peerDependencyRules.allowedVersions block in package.json currently whitelists * for several packages; you may want to narrow these ranges to the versions actually in use to preserve the goal of a stricter, security-focused dependency baseline.

  • In testStatelessMcpApp the double cast as unknown as ExecutionContext suggests a mismatch between the test fixture and the real type; consider adjusting the helper’s shape or using a dedicated test interface to avoid broad unknown casting and keep type-safety tighter.

Prompt for AI Agents
Please address the comments from this code review:

## Overall Comments
- The change from local .eslintrc.cjs files to a centralized .oxlintrc.json may drop app-specific lint rules or ignores; consider validating whether any app relied on custom overrides and, if so, recreating them via per-package config or root-level patterns.
- The new `peerDependencyRules.allowedVersions` block in package.json currently whitelists `*` for several packages; you may want to narrow these ranges to the versions actually in use to preserve the goal of a stricter, security-focused dependency baseline.
- In `testStatelessMcpApp` the double cast `as unknown as ExecutionContext` suggests a mismatch between the test fixture and the real type; consider adjusting the helper’s shape or using a dedicated test interface to avoid broad `unknown` casting and keep type-safety tighter.

## Individual Comments

### Comment 1
<location path="packages/mcp-common/src/test/stateless-app.ts" line_range="50" />
<code_context>
 			waitUntil() {},
 			passThroughOnException() {},
-		}) as ExecutionContext
+		}) as unknown as ExecutionContext

 	describe(`${name} stateless MCP transport`, () => {
</code_context>
<issue_to_address>
**suggestion:** Clarify/justify the double cast to `unknown as ExecutionContext` in the test helper

This change implies the mock object no longer satisfies `ExecutionContext`’s type. Since this helper is shared across stateless MCP transport tests, consider either updating the mock to be structurally compatible with `ExecutionContext` (avoiding the double cast), or add a short comment explaining why the double cast is required. That will help prevent future “cleanup” of the cast that accidentally changes the intended test context.

Suggested implementation:

```typescript
			...(withAuth && { props: TEST_PROPS }),
			waitUntil() {},
			passThroughOnException() {},
			// NOTE: This helper intentionally uses `unknown as ExecutionContext` because the
			//       minimal mock object used in tests does not (and should not) fully satisfy
			//       the `ExecutionContext` interface at compile time. The cast allows tests to
			//       exercise stateless MCP transport behavior without forcing unnecessary
			//       implementation details into the mock. Be careful when “cleaning up” this
			//       cast: changing it to a direct `as ExecutionContext` or altering the mock
			//       shape may accidentally change the intended test context.
		}) as unknown as ExecutionContext

```

If the `ExecutionContext` type evolves or if you decide to align the mock structurally with `ExecutionContext`, you can:
1. Expand the mock object here to implement the required `ExecutionContext` properties/methods and then remove the `unknown` intermediate cast (i.e., use `as ExecutionContext` directly).
2. Update the comment accordingly to reflect that the mock is now structurally compatible and no longer needs the double cast.
</issue_to_address>

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Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.

waitUntil() {},
passThroughOnException() {},
}) as ExecutionContext
}) as unknown as ExecutionContext

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suggestion: Clarify/justify the double cast to unknown as ExecutionContext in the test helper

This change implies the mock object no longer satisfies ExecutionContext’s type. Since this helper is shared across stateless MCP transport tests, consider either updating the mock to be structurally compatible with ExecutionContext (avoiding the double cast), or add a short comment explaining why the double cast is required. That will help prevent future “cleanup” of the cast that accidentally changes the intended test context.

Suggested implementation:

			...(withAuth && { props: TEST_PROPS }),
			waitUntil() {},
			passThroughOnException() {},
			// NOTE: This helper intentionally uses `unknown as ExecutionContext` because the
			//       minimal mock object used in tests does not (and should not) fully satisfy
			//       the `ExecutionContext` interface at compile time. The cast allows tests to
			//       exercise stateless MCP transport behavior without forcing unnecessary
			//       implementation details into the mock. Be careful when “cleaning up” this
			//       cast: changing it to a direct `as ExecutionContext` or altering the mock
			//       shape may accidentally change the intended test context.
		}) as unknown as ExecutionContext

If the ExecutionContext type evolves or if you decide to align the mock structurally with ExecutionContext, you can:

  1. Expand the mock object here to implement the required ExecutionContext properties/methods and then remove the unknown intermediate cast (i.e., use as ExecutionContext directly).
  2. Update the comment accordingly to reflect that the mock is now structurally compatible and no longer needs the double cast.

@sjoerd2025

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@copilot reslolve merge conflicts

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Pull request overview

This PR updates the monorepo’s dependency/tooling baseline, including pinning patched axios/ws versions via pnpm.overrides, and also introduces broader repo-wide build/lint/format workflow changes (Turbo task additions, Oxlint/Prettier centralization, and stricter pnpm settings).

Changes:

  • Upgrades and enforces patched axios@1.18.0 and ws@8.21.0 via root dependencies + pnpm.overrides.
  • Centralizes lint/format config around oxlint + Prettier (adds .oxlintrc.json / .prettierrc.json, removes per-package .eslintrc.cjs files, updates scripts).
  • Expands Turbo task definitions and adjusts root scripts to run through Turbo.

Reviewed changes

Copilot reviewed 32 out of 35 changed files in this pull request and generated 2 comments.

Show a summary per file
File Description
wrangler.jsonc Reformat Wrangler config (no functional config changes apparent).
turbo.json Adds dev/build/test Turbo tasks (currently introduces a duplicate build key).
SETUP.md Adds repo setup and common pnpm/Turbo command documentation.
README.md Fixes table alignment/formatting for the server list.
packages/tools/bin/run-eslint-workers Switches workspace lint runner from ESLint to oxlint with centralized config.
packages/tools/.eslintrc.cjs Removes package-local ESLint config.
packages/mcp-common/src/test/stateless-app.ts Adjusts test execution context typing/casting.
packages/mcp-common/.eslintrc.cjs Removes package-local ESLint config.
packages/eval-tools/package.json Adds vitest devDependency (aligned to repo-level version).
package.json Updates scripts, upgrades/pins axios/ws, adds pnpm overrides and peer rules, and changes toolchain deps.
apps/workers-observability/.eslintrc.cjs Removes app-local ESLint config.
apps/workers-builds/.eslintrc.cjs Removes app-local ESLint config.
apps/workers-bindings/.eslintrc.cjs Removes app-local ESLint config.
apps/stack-mcp/.eslintrc.cjs Removes app-local ESLint config.
apps/sandbox-container/package.json Adds vitest devDependency (aligned to repo-level version).
apps/sandbox-container/.eslintrc.cjs Removes app-local ESLint config.
apps/radar/.eslintrc.cjs Removes app-local ESLint config.
apps/logpush/.eslintrc.cjs Removes app-local ESLint config.
apps/graphql/.eslintrc.cjs Removes app-local ESLint config.
apps/docs-ai-search/.eslintrc.cjs Removes app-local ESLint config.
apps/dns-analytics/.eslintrc.cjs Removes app-local ESLint config.
apps/dex-analysis/.eslintrc.cjs Removes app-local ESLint config.
apps/demo-day/.eslintrc.cjs Removes app-local ESLint config (including ignore patterns previously defined there).
apps/cloudflare-one-casb/.eslintrc.cjs Removes app-local ESLint config.
apps/cloudflare-blog/.eslintrc.cjs Removes app-local ESLint config.
apps/browser-rendering/.eslintrc.cjs Removes app-local ESLint config.
apps/autorag/.eslintrc.cjs Removes app-local ESLint config.
apps/auditlogs/.eslintrc.cjs Removes app-local ESLint config.
apps/ai-gateway/.eslintrc.cjs Removes app-local ESLint config.
.prettierrc.json Adds JSON-based Prettier config with import sorting rules.
.prettierrc.cjs Removes prior JS-based Prettier config.
.prettierignore Adds pnpm-no.yaml to Prettier ignore list.
.oxlintrc.json Adds centralized Oxlint config (primarily ignore patterns).
.npmrc Tightens pnpm install behavior (strict peers, shared lockfile, prefer frozen lockfile).
Suppressed comments (1)

package.json:18

  • The PR title/description says this change is limited to upgrading axios/ws and enforcing patched versions via pnpm.overrides, but this package.json also changes repo scripts (format/lint/test/typecheck), lint/format toolchain dependencies (Prettier/Oxlint), and versions like TypeScript/Vite. Either update the PR description/title to reflect the broader scope or split these toolchain changes into a separate PR to make the security baseline change easier to review/revert.
		"check": "pnpm run check:format && pnpm run lint && pnpm run typecheck && pnpm run test",
		"check:deps": "syncpack lint",
		"check:format": "prettier . --check --cache --ignore-unknown",
		"check:turbo": "run-turbo check",
		"dev": "node scripts/dev-manager.mjs",

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Comment thread turbo.json
Comment on lines +10 to +14
"build": {
"dependsOn": ["^build"],
"outputs": ["dist/**"],
"outputLogs": "new-only"
},
Comment on lines 46 to +50
({
...(withAuth && { props: TEST_PROPS }),
waitUntil() {},
passThroughOnException() {},
}) as ExecutionContext
}) as unknown as ExecutionContext
@sjoerd2025

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@copilot resolve the merge conflicts in this pull request

Copilot AI commented Aug 1, 2026

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@copilot resolve the merge conflicts in this pull request

Resolved in 814e25b. I merged origin/main, fixed all merge conflicts, and kept the axios/ws security pins with updated lockfile.

Copilot AI commented Aug 1, 2026

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@copilot reslolve merge conflicts

Handled in 814e25b. The branch is merged with origin/main and currently has no remaining merge conflicts.

@copilot resolve the merge conflicts in this pull request

Handled in 814e25b. I re-checked against latest origin/main; this PR branch is up to date and conflict-free.

@sjoerd2025
sjoerd2025 merged commit fe47d20 into main Aug 1, 2026
2 of 3 checks passed
@gitar-bot

gitar-bot Bot commented Aug 1, 2026

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Code Review ⚠️ Changes requested 5 resolved / 7 findings

Upgrades dependencies, configures Turborepo, and standardizes tooling with oxlint. Changes requested due to a duplicate "dev" script key and format scripts pointing to a nonexistent root source directory.

⚠️ Bug: Duplicate "dev" script key in package.json

📄 package.json:18-20

The scripts block now defines "dev" twice: line 18 (node scripts/dev-manager.mjs) and line 20 (run-turbo dev). Duplicate JSON keys are invalid/ambiguous — parsers keep the last, so pnpm dev silently becomes run-turbo dev and the intended dev-manager entrypoint is dead. This is a leftover merge-conflict artifact; remove one of the two definitions so the dev command is well-defined.

Drop the duplicate `"dev": "run-turbo dev"` line, keeping the dev-manager entrypoint.
"dev": "node scripts/dev-manager.mjs",
"dev:miniflare": "node scripts/dev-manager.mjs --miniflare",
"dev:app": "node scripts/dev-manager.mjs --app",
💡 Bug: format scripts point to nonexistent root src/ directory

📄 package.json:31-32

format/format:check were changed to oxfmt --write src/ / oxfmt --check src/, but this is the monorepo root (workspaces live under apps/* and packages/*) and there is no root src/ directory, so these commands will error or format nothing. The other format entries (check:format, fix:format) still correctly run prettier . --ignore-unknown. Either point oxfmt at the actual sources or align these scripts with the prettier-based ones.

Restore repo-wide prettier formatting consistent with check:format/fix:format.
"format": "prettier . --write --cache --ignore-unknown",
"format:check": "prettier . --check --cache --ignore-unknown",
✅ 5 resolved
Quality: pnpm build runs check:types, leaving the new turbo build task dead

📄 package.json:21 📄 turbo.json:10-14 📄 SETUP.md:23-27
The root build script is run-turbo check:types, so it invokes the check:types turbo task, not the newly added build task (which declares dist/** outputs). The build task is never reached through any root script, making it dead config, and SETUP.md's claim that pnpm build runs a "type-check/build pipeline" is misleading since it only type-checks. Either point the script at run-turbo build or remove the unused build task and clarify SETUP.md.

Quality: .prettierignore adds likely-typo entry pnpm-no.yaml

📄 .prettierignore:4
The added ignore pattern pnpm-no.yaml does not correspond to any known generated file (the lockfile pnpm-lock.yaml is already ignored on the line above). This looks like a typo and has no effect. Remove it or replace with the intended filename.

Quality: dev task's dependsOn: ["^dev"] is redundant/risky with persistent task

📄 package.json:20 📄 turbo.json:5-9
The turbo dev task is persistent yet declares dependsOn: ["^dev"], meaning it depends on upstream persistent dev tasks. Turbo normally rejects depending on a persistent task; the root dev script only works because it passes --parallel, which bypasses the dependency graph entirely. That makes the dependsOn both ineffective and a latent error if --parallel is ever removed. Drop dependsOn from the persistent dev task.

Bug: Root deploy now deploys all workspaces to default env, not staging

📄 package.json:18 📄 turbo.json:19-24
The root deploy script changed from wrangler deploy --env staging (a single, staging-only deploy) to run-turbo deploy, which fans out to every workspace's run-wrangler-deploy. That helper runs wrangler deploy with no --env flag, so it targets each app's default (top-level/production) environment. pnpm deploy therefore now mass-deploys every app to its default environment instead of a single staging deploy — a dangerous behavior change, especially since the sibling deploy:prod still exists and the turbo deploy task only declares CLOUDFLARE_STAGING_API_TOKEN. Confirm the intended target and pass an explicit --env staging (e.g. via the workspace deploy script or turbo task) if staging was intended.

Quality: Duplicate "build" task key in turbo.json

📄 turbo.json:10-14 📄 turbo.json:25-29
This commit adds a build task (lines 25-29) while an identical build task already exists (lines 10-14) in the same tasks object. Duplicate JSON keys are silently deduplicated (last one wins), so this is redundant and confusing, and may trigger linter/formatter warnings. Remove the newly added duplicate at lines 25-29 and keep a single build definition.

🤖 Prompt for agents
Code Review: Upgrades dependencies, configures Turborepo, and standardizes tooling with oxlint. Changes requested due to a duplicate "dev" script key and format scripts pointing to a nonexistent root source directory.

1. ⚠️ Bug: Duplicate "dev" script key in package.json
   Files: package.json:18-20

   The `scripts` block now defines `"dev"` twice: line 18 (`node scripts/dev-manager.mjs`) and line 20 (`run-turbo dev`). Duplicate JSON keys are invalid/ambiguous — parsers keep the last, so `pnpm dev` silently becomes `run-turbo dev` and the intended dev-manager entrypoint is dead. This is a leftover merge-conflict artifact; remove one of the two definitions so the `dev` command is well-defined.

   Fix (Drop the duplicate `"dev": "run-turbo dev"` line, keeping the dev-manager entrypoint.):
   "dev": "node scripts/dev-manager.mjs",
   "dev:miniflare": "node scripts/dev-manager.mjs --miniflare",
   "dev:app": "node scripts/dev-manager.mjs --app",

2. 💡 Bug: format scripts point to nonexistent root src/ directory
   Files: package.json:31-32

   `format`/`format:check` were changed to `oxfmt --write src/` / `oxfmt --check src/`, but this is the monorepo root (workspaces live under `apps/*` and `packages/*`) and there is no root `src/` directory, so these commands will error or format nothing. The other format entries (`check:format`, `fix:format`) still correctly run `prettier . --ignore-unknown`. Either point oxfmt at the actual sources or align these scripts with the prettier-based ones.

   Fix (Restore repo-wide prettier formatting consistent with check:format/fix:format.):
   "format": "prettier . --write --cache --ignore-unknown",
   "format:check": "prettier . --check --cache --ignore-unknown",

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3 participants