⬆️ Upgrade all dependencies

[NatoBoram]

This bug prevented auto-updating dependencies:

• fix: support exactOptionalPropertyTypes in Transport interface modelcontextprotocol/typescript-sdk#1507

Changelog

Comprehensive dependency upgrades and MCP SDK typing/config fixes.

Added

• ✨ Split based MCP server into based_http and based_stdio in .vscode/mcp.json
• ➕ Add patch patches/@modelcontextprotocol__sdk.patch to adjust transport typings

Changed

• ⬆️ Bump @modelcontextprotocol/sdk in package.json
• ⬆️ Bump commander, cors, express, and zod in package.json
• ⬆️ Bump devDependencies (TypeScript, ESLint, Vitest, types) in package.json
• 👽️ Remove sessionIdGenerator option from StreamableHTTPServerTransport instantiation in src/mcp/app.ts
• 🔧 Register patched dependency entry for @modelcontextprotocol/sdk in pnpm-workspace.yaml
• ♻️ Replace imports from zod/v3 with zod across src/zod/* and .github/instructions/zod.instructions.md

Fixed

• 🐛 Make optional transport callbacks (onclose, onerror, onmessage, sessionId) explicitly accept undefined in dist/esm/shared/transport.d.ts via the SDK patch

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

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Walkthrough

Splits the single based server entry into explicit based_http and based_stdio, removes several contextual servers, updates dependency versions, adds a patch for @modelcontextprotocol/sdk to relax type optionality, and removes sessionIdGenerator from the StreamableHTTPServerTransport constructor call.

Changes

Cohort / File(s)	Summary
Server configuration .vscode/mcp.json	Replaces unified based server with based_http (HTTP) and based_stdio (STDIO); removes contextual servers (context7, deepwiki, github, grep).
Workspace & patches pnpm-workspace.yaml, patches/@modelcontextprotocol__sdk.patch	Adds patch entry for @modelcontextprotocol/sdk and normalizes quoting; patch updates dist/esm/shared/transport.d.ts to allow undefined for callback and sessionId types.
Dependencies package.json	Bumps runtime and dev dependencies (including @modelcontextprotocol/sdk, commander, cors, express, zod, TypeScript toolchain, linters, and test tooling).
Application code src/mcp/app.ts	Removes sessionIdGenerator option when constructing StreamableHTTPServerTransport, leaving enableJsonResponse: true.
Zod import fixes src/zod/convert.ts, src/zod/object_type.ts, src/zod/uuid.ts, .github/instructions/zod.instructions.md	Replaces imports from zod/v3 with zod for type and value imports; no runtime changes.

Possibly related PRs

• ⬆️ Bump zod from 3.25.76 to 4.1.13 #153: Directly related — modifies zod usage/versioning and aligns with import changes from zod/v3 to zod.
• ⬆️ Bump @types/node from 24.10.1 to 25.0.3 #160: Related — updates @types/node, matching devDependency bumps in this PR.
• ⬆️ Bump markdownlint-cli2 from 0.19.1 to 0.20.0 #163: Related — updates markdownlint-cli2, matching devDependency bumps in this PR.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The PR title '⬆️ Upgrade all dependencies' correctly uses the upgrade emoji and clearly summarizes the main objective of upgrading dependencies across the project.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Gitmoji Commits	✅ Passed	The single commit in the PR starts with a valid gitmoji (🔧) and correctly represents configuration and import refactoring changes.
Git Flow	✅ Passed	The pull request's branch names comply with Git Flow configuration. Source branch 'feature/update-mcp-sdk' correctly uses the 'feature/' prefix and target branch 'main' is the configured master/develop branch.

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✨ Finishing Touches

• 📝 Generate docstrings (stacked PR)
• 📝 Generate docstrings (commit on current branch)

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch feature/update-mcp-sdk

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