[pull] main from modelcontextprotocol:main

README.md

@@ -241,7 +241,6 @@ Official integrations are maintained by companies building production ready MCP
 - <img height="14" width="14" src="https://raw.githubusercontent.com/rust-mcp-stack/mcp-discovery/refs/heads/main/docs/_media/mcp-discovery-logo.png" alt="mcp-discovery logo" /> **[MCP Discovery](https://github.com/rust-mcp-stack/mcp-discovery)** - A lightweight CLI tool built in Rust for discovering MCP server capabilities.
 - <img height="12" width="12" src="https://googleapis.github.io/genai-toolbox/favicons/favicon.ico" alt="MCP Toolbox for Databases Logo" /> **[MCP Toolbox for Databases](https://github.com/googleapis/genai-toolbox)** - Open source MCP server specializing in easy, fast, and secure tools for Databases. Supports  AlloyDB, BigQuery, Bigtable, Cloud SQL, Dgraph, MySQL, Neo4j, Postgres, Spanner, and more.
 - <img height="12" width="12" src="https://www.meilisearch.com/favicon.ico" alt="Meilisearch Logo" /> **[Meilisearch](https://github.com/meilisearch/meilisearch-mcp)** - Interact & query with Meilisearch (Full-text & semantic search API)
-- <img height="12" width="12" src="https://memgraph.com/favicon.png" alt="Memgraph Logo" /> **[Memgraph](https://github.com/memgraph/mcp-memgraph)** - Query your data in [Memgraph](https://memgraph.com/) graph database.
 - <img height="12" width="12" src="https://memgraph.com/favicon.png" alt="Memgraph Logo" /> **[Memgraph](https://github.com/memgraph/ai-toolkit/tree/main/integrations/mcp-memgraph)** - Query your data in [Memgraph](https://memgraph.com/) graph database.
 - <img height="12" width="12" src="https://www.mercadolibre.com.ar/favicon.ico" alt="MercadoLibre Logo" /> **[Mercado Libre](https://mcp.mercadolibre.com/)** - Mercado Libre's official MCP server.
 - <img height="12" width="12" src="https://www.mercadopago.com/favicon.ico" alt="MercadoPago Logo" /> **[Mercado Pago](https://mcp.mercadopago.com/)** - Mercado Pago's official MCP server.
@@ -1069,6 +1068,7 @@ These are high-level frameworks that make it easier to build MCP servers or clie
 * **[mcp_sse (Elixir)](https://github.com/kEND/mcp_sse)** An SSE implementation in Elixir for rapidly creating MCP servers.
 * **[Next.js MCP Server Template](https://github.com/vercel-labs/mcp-for-next.js)** (Typescript) - A starter Next.js project that uses the MCP Adapter to allow MCP clients to connect and access resources.
 * **[Quarkus MCP Server SDK](https://github.com/quarkiverse/quarkus-mcp-server)** (Java)
+- **[R mcptools](https://github.com/posit-dev/mcptools)** - An R SDK for creating R-based MCP servers and retrieving functionality from third-party MCP servers as R functions.
 * **[SAP ABAP MCP Server SDK](https://github.com/abap-ai/mcp)** - Build SAP ABAP based MCP servers. ABAP 7.52 based with 7.02 downport; runs on R/3 & S/4HANA on-premises, currently not cloud-ready.
 * **[Spring AI MCP Server](https://docs.spring.io/spring-ai/reference/api/mcp/mcp-server-boot-starter-docs.html)** - Provides auto-configuration for setting up an MCP server in Spring Boot applications.
 * **[Template MCP Server](https://github.com/mcpdotdirect/template-mcp-server)** - A CLI tool to create a new Model Context Protocol server project with TypeScript support, dual transport options, and an extensible structure
@@ -1091,6 +1091,7 @@ These are high-level frameworks that make it easier to build MCP servers or clie
 
 Additional resources on MCP.
 
+- **[A2A-MCP Java Bridge](https://github.com/vishalmysore/a2ajava)** - A2AJava brings powerful A2A-MCP integration directly into your Java applications. It enables developers to annotate standard Java methods and instantly expose them as MCP Server, A2A-discoverable actions — with no boilerplate or service registration overhead.
 - **[AiMCP](https://www.aimcp.info)** - A collection of MCP clients&servers to find the right mcp tools by **[Hekmon](https://github.com/hekmon8)**
 - **[Awesome Crypto MCP Servers by badkk](https://github.com/badkk/awesome-crypto-mcp-servers)** - A curated list of MCP servers by **[Luke Fan](https://github.com/badkk)**
 - **[Awesome MCP Servers by appcypher](https://github.com/appcypher/awesome-mcp-servers)** - A curated list of MCP servers by **[Stephen Akinyemi](https://github.com/appcypher)**

src/filesystem/README.md

@@ -9,11 +9,11 @@ Node.js server implementing Model Context Protocol (MCP) for filesystem operatio
 - Move files/directories
 - Search files
 - Get file metadata
-- Dynamic directory access control via [Roots](https://modelcontextprotocol.io/docs/concepts/roots)
+- Dynamic directory access control via [Roots](https://modelcontextprotocol.io/docs/learn/client-concepts#roots)
 
 ## Directory Access Control
 
-The server uses a flexible directory access control system. Directories can be specified via command-line arguments or dynamically via [Roots](https://modelcontextprotocol.io/docs/concepts/roots).
+The server uses a flexible directory access control system. Directories can be specified via command-line arguments or dynamically via [Roots](https://modelcontextprotocol.io/docs/learn/client-concepts#roots).
 
 ### Method 1: Command-line Arguments
 Specify Allowed directories when starting the server:
@@ -22,7 +22,7 @@ mcp-server-filesystem /path/to/dir1 /path/to/dir2
 ```
 
 ### Method 2: MCP Roots (Recommended)
-MCP clients that support [Roots](https://modelcontextprotocol.io/docs/concepts/roots) can dynamically update the Allowed directories. 
+MCP clients that support [Roots](https://modelcontextprotocol.io/docs/learn/client-concepts#roots) can dynamically update the Allowed directories. 
 
 Roots notified by Client to Server, completely replace any server-side Allowed directories when provided.