chore: Add a new generic copilot-instructions.md to make copilot more useful on reviews (#572)

Author: kmruiz

.github/copilot-instructions.md

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+# Project Overview
+
+This project is a server implementing the MCP (Model Context Protocol) that allows users to interact with their MongoDB clusters
+and MongoDB Atlas accounts. It is built using TypeScript, Node.js and the official Anthropic
+@modelcontextprotocol/sdk SDK.
+
+## Folder Structure
+
+- `/src`: Contains the source code of the MCP Server.
+- `/src/tools`: Contains the implementation of MCP tools.
+- `/src/tools/atlas/`: Contains the implementation of MCP tools that are specific to MongoDB Atlas.
+- `/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.
+- `/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.
+
+## Libraries and Frameworks
+
+- Zod for message and schema validation.
+- Express for the HTTP Transport implementation.
+- mongosh NodeDriverServiceProvider for connecting to MongoDB.
+- vitest for testing.
+- @modelcontextprotocol/sdk for the protocol implementation.
+
+## Coding Standards
+
+- For declarations, use types. For usage, rely on type inference unless it is not clear enough.
+- Always follow the eslint and prettier rule formats specified in `.eslint.config.js` and `.prettierrc.json`.
+- Use classes for stateful components and functions for stateless pure logic.
+- Use dependency injection to provide dependencies between components.
+- Avoid using global variables as much as possible.
+- New functionality MUST be under test.
+  - Tools MUST HAVE integration tests.
+  - Tools MUST HAVE unit tests.
+  - Tools MAY HAVE accuracy tests.
+
+## Architectural Guidelines and Best Practices
+
+Every agent connected to the MCP Server has a Session object attached to it. The Session is the main entrypoint for
+dependencies to other components. Any component that MUST be used by either a tool or a resource MUST be provided
+through the Session.
+
+### Guidelines for All Tools
+
+- The name of the tool should describe an action: `create-collection`, `insert-many`.
+- The description MUST be a simple and accurate prompt that defines what the tool does in an unambiguous way.
+- All tools MUST provide a Zod schema that clearly specifies the API of the tool.
+- The Operation type MUST be clear:
+  - `metadata`: Reads metadata for an entity (for example, a cluster). Example: CollectionSchema.
+  - `read`: Reads information from a cluster or Atlas.
+  - `create`: Creates resources, like a collection or a cluster.
+  - `delete`: Deletes resources or documents, like collections, documents or clusters.
+  - `update`: Modifies resources or documents, like collections, documents or clusters.
+  - `connects`: Connects to a MongoDB cluster.
+- If a new tool is added, or the tool description is modified, the accuracy tests MUST be updated too.
+
+### Guidelines for MongoDB Tools
+
+- The tool category MUST be `mongodb`.
+- They MUST call `this.ensureConnected()` before attempting to query MongoDB.
+- They MUST return content sanitized using `formatUntrustedData`.
+- Documents should be serialized with `EJSON.stringify`.
+- Ensure there are proper timeout mechanisms to avoid long-running queries that can affect the server.
+- Tools that require elicitation MUST implement `getConfirmationMessage` and provide an easy-to-understand message for a human running the operation.
+  - If a tool requires elicitation, it must be added to `src/common/config.ts` in the `confirmationRequiredTools` list in the defaultUserConfig.
+
+### Guidelines for Atlas Tools
+
+- The tool category MUST be `atlas`.