refactor: move to v2 structure MCP-373

.github/copilot-instructions.md

@@ -12,7 +12,7 @@ and MongoDB Atlas accounts. It is built using TypeScript, Node.js and the offici
 - `/src/tools/mongodb/`: Contains the implementation of MCP tools that are specific to MongoDB clusters.
 - `/src/resources`: Contains the implementation of MCP Resources.
 - `/tests`: Contains the test code for the MCP Server.
-- `/tests/accuracy`: Contains the test code for the accuracy tests, that use different models to ensure that tools have reliable descriptions.
+- `/packages/accuracy-tests`: Contains the test code for the accuracy tests, that use different models to ensure that tools have reliable descriptions.
 - `/tests/integration`: Contains tests that start the MCP Server and interact with it to ensure that functionality is correct.
 - `/tests/unit`: Contains simple unit tests to cover specific functionality of the MCP Server.
 

.github/workflows/accuracy-tests.yml

@@ -44,6 +44,8 @@ jobs:
           cache: "pnpm"
       - name: Install dependencies
         run: pnpm install --frozen-lockfile
+      - name: Build
+        run: pnpm run build
       - name: Run accuracy tests
         run: pnpm run test:accuracy
       - name: Upload accuracy test summary

.github/workflows/check.yml

@@ -23,6 +23,8 @@ jobs:
           cache: "pnpm"
       - name: Install dependencies
         run: pnpm install --frozen-lockfile
+      - name: Build
+        run: pnpm run build
       - name: Run style check
         run: pnpm run check
 
@@ -40,6 +42,8 @@ jobs:
           cache: "pnpm"
       - name: Install dependencies
         run: pnpm install --frozen-lockfile
+      - name: Build
+        run: pnpm run build
       - run: pnpm run generate
 
   check-dep:
@@ -55,11 +59,14 @@ jobs:
         with:
           node-version-file: package.json
           cache: "pnpm"
-      - name: Install dependencies, build and remove dev dependencies
+      - name: Install dependencies and build
         run: |
           pnpm install --frozen-lockfile
+          pnpm run build
+      - name: Remove dev dependencies
+        run: |
           rm -rf node_modules
           pnpm pkg set scripts.prepare="exit 0"
           pnpm install --prod --frozen-lockfile
       - name: List available tools
-        run: pnpm dlx @modelcontextprotocol/inspector@0.16.5 --cli --method tools/list -- node dist/esm/index.js
+        run: pnpm dlx @modelcontextprotocol/inspector@0.16.5 --cli --method tools/list -- node packages/mongodb-mcp-server/dist/esm/index.js

.github/workflows/code-health-fork.yml

@@ -41,6 +41,8 @@ jobs:
           cache: "pnpm"
       - name: Install dependencies
         run: pnpm install --frozen-lockfile
+      - name: Build
+        run: pnpm run build
       # TODO: Re-enable on Windows once the silent worker fork crash / mongod cleanup
       # leak is resolved. See MCP-495.
       - name: Run tests
@@ -63,10 +65,12 @@ jobs:
           cache: "pnpm"
       - name: Install dependencies
         run: pnpm install --frozen-lockfile
+      - name: Build
+        run: pnpm run build
       - name: Pre-pull Atlas Local images
         run: |
           docker pull mongodb/mongodb-atlas-local:preview &
           docker pull mongodb/mongodb-atlas-local:latest &
           wait
       - name: Run tests
-        run: pnpm test -- tests/integration/tools/atlas-local/
+        run: pnpm test -- packages/integration-tests/src/tools/atlas-local/

.github/workflows/code-health-long-running.yml

@@ -24,12 +24,14 @@ jobs:
           cache: "pnpm"
       - name: Install dependencies
         run: pnpm install --frozen-lockfile
+      - name: Build
+        run: pnpm run build
       - name: Run tests
         env:
           MDB_MCP_API_CLIENT_ID: ${{ secrets.TEST_ATLAS_CLIENT_ID }}
           MDB_MCP_API_CLIENT_SECRET: ${{ secrets.TEST_ATLAS_CLIENT_SECRET }}
           MDB_MCP_API_BASE_URL: ${{ vars.TEST_ATLAS_BASE_URL }}
-        run: pnpm test tests/integration/tools/atlas --project=long-running-tests
+        run: pnpm test packages/integration-tests/src/tools/atlas --project=long-running-tests
       - name: Upload test results
         uses: actions/upload-artifact@v7.0.1
         if: always()

.github/workflows/code-health.yml

@@ -42,6 +42,8 @@ jobs:
           cache: "pnpm"
       - name: Install dependencies
         run: pnpm install --frozen-lockfile
+      - name: Build
+        run: pnpm run build
       # TODO: Re-enable on Windows once the silent worker fork crash / mongod cleanup
       # leak is resolved. See MCP-495.
       - name: Run tests
@@ -75,12 +77,14 @@ jobs:
           cache: "pnpm"
       - name: Install dependencies
         run: pnpm install --frozen-lockfile
+      - name: Build
+        run: pnpm run build
       - name: Run tests
         env:
           MDB_MCP_API_CLIENT_ID: ${{ secrets.TEST_ATLAS_CLIENT_ID }}
           MDB_MCP_API_CLIENT_SECRET: ${{ secrets.TEST_ATLAS_CLIENT_SECRET }}
           MDB_MCP_API_BASE_URL: ${{ vars.TEST_ATLAS_BASE_URL }}
-        run: pnpm test tests/integration/tools/atlas/
+        run: pnpm test packages/integration-tests/src/tools/atlas/
       - name: Upload test results
         uses: actions/upload-artifact@v7.0.1
         if: always()
@@ -110,7 +114,7 @@ jobs:
           docker pull mongodb/mongodb-atlas-local:latest &
           wait
       - name: Run tests
-        run: pnpm test tests/integration/tools/atlas-local/
+        run: pnpm test packages/integration-tests/src/tools/atlas-local/
       - name: Upload test results
         uses: actions/upload-artifact@v7.0.1
         if: always()
@@ -134,16 +138,18 @@ jobs:
           cache: "pnpm"
       - name: Install dependencies
         run: pnpm install --frozen-lockfile
+      - name: Build
+        run: pnpm run build
       - name: Install Playwright Chromium
-        run: pnpm --filter browser run install:browser
+        run: pnpm --filter @mongodb-js/mcp-browser-tests run install:browser
       - name: Run browser tests
         run: pnpm run test:browser
       - name: Upload test results
         if: always()
         uses: actions/upload-artifact@v7.0.1
         with:
           name: browser-test-results
-          path: coverage/tests/browser/lcov.info
+          path: coverage/packages/browser-tests/lcov.info
 
   coverage:
     name: Report Coverage

.github/workflows/mcpb.yml

@@ -27,6 +27,8 @@ jobs:
           cache: "pnpm"
       - name: Install dependencies
         run: pnpm install --frozen-lockfile
+      - name: Build
+        run: pnpm run build
       - name: Validate manifest
         run: pnpm run validate:mcpb
       - name: Build .mcpb

.gitignore

@@ -1,5 +1,6 @@
 dist
 node_modules
+.eslintcache
 
 .vscode/mcp.json
 .github/prompts/*
@@ -10,12 +11,12 @@ node_modules
 # Sensitive
 state.json
 
-tests/tmp
+**/tmp
 coverage
 # Generated assets by accuracy runs
 .accuracy
 
-temp
+**/temp
 .DS_Store
 
 # Development tool files
@@ -25,3 +26,8 @@ yalc.lock
 # .mcpb build artifacts
 mcpb-build/
 dist-mcpb/
+
+.claude
+CLAUDE.md
+
+**/*.tsbuildinfo

.npmrc

@@ -1 +1,2 @@
 git-tag-version=false
+workspace-concurrency=8

.prettierignore

@@ -1,12 +1,11 @@
 dist
-coverage
-package-lock.json
-tests/tmp
-src/common/atlas/openapi.d.ts
-pnpm-lock.yaml
-src/ui/lib/tools
+node_modules
+*.lock
+resources/
 src/ui/lib/loaders.ts
 temp
-api-extractor/reports
+**/reports/*.api.md
+**/reports/*.api.json
 .github/workflows/*.lock.yml
-packaging/mcpb/manifest.json
+**/packaging/mcpb/manifest.json
+pnpm-lock.yaml

CONTRIBUTING.md

@@ -127,7 +127,7 @@ npx @modelcontextprotocol/inspector -- node dist/esm/index.js
 
 ## Making public API changes
 
-To ensure no unintentional public API changes are introduced, the project uses [API Extractor](https://api-extractor.com/) to track the public-facing API across all package entry points (`.`, `./web`, `./tools`, `./ui`). The generated API report files live in `api-extractor/reports/` and are checked into source control.
+To ensure no unintentional public API changes are introduced, the project uses [API Extractor](https://api-extractor.com/) to track the public-facing API across package entry points (`.`, `./web`, `./ui`) and the internal tools surface (`src/tools/index.ts`, report only). The generated API report files live in `api-extractor/reports/` and are checked into source control.
 
 ### Workflow when changing the public API