docs: Update VS Code installation instructions to use mcp.json

- Replace outdated 'Preferences: Open Settings (JSON)' instructions
- Add proper guidance for 'MCP: Open User Configuration' command
- Update JSON examples to remove mcp wrapper key
- Clarify user vs workspace configuration methods
- Fixes issue with outdated documentation across all servers

Affects: sequentialthinking, filesystem, memory, everything, git

src/everything/README.md

@@ -160,17 +160,20 @@ For quick installation, use of of the one-click install buttons below...
 
 [![Install with Docker in VS Code](https://img.shields.io/badge/VS_Code-Docker-0098FF?style=flat-square&logo=visualstudiocode&logoColor=white)](https://insiders.vscode.dev/redirect/mcp/install?name=everything&config=%7B%22command%22%3A%22docker%22%2C%22args%22%3A%5B%22run%22%2C%22-i%22%2C%22--rm%22%2C%22mcp%2Feverything%22%5D%7D) [![Install with Docker in VS Code Insiders](https://img.shields.io/badge/VS_Code_Insiders-Docker-24bfa5?style=flat-square&logo=visualstudiocode&logoColor=white)](https://insiders.vscode.dev/redirect/mcp/install?name=everything&config=%7B%22command%22%3A%22docker%22%2C%22args%22%3A%5B%22run%22%2C%22-i%22%2C%22--rm%22%2C%22mcp%2Feverything%22%5D%7D&quality=insiders)
 
-For manual installation, add the following JSON block to your User Settings (JSON) file in VS Code. You can do this by pressing `Ctrl + Shift + P` and typing `Preferences: Open User Settings (JSON)`.
+For manual installation, you can configure the MCP server using one of these methods:
 
-Optionally, you can add it to a file called `.vscode/mcp.json` in your workspace. This will allow you to share the configuration with others.
+**Method 1: User Configuration (Recommended)**
+Add the configuration to your user-level MCP configuration file. Open the Command Palette (`Ctrl + Shift + P`) and run `MCP: Open User Configuration`. This will open your user `mcp.json` file where you can add the server configuration.
 
-> Note that the `mcp` key is not needed in the `.vscode/mcp.json` file.
+**Method 2: Workspace Configuration**
+Alternatively, you can add the configuration to a file called `.vscode/mcp.json` in your workspace. This will allow you to share the configuration with others.
+
+> Note that the `servers` object should be at the root level in `mcp.json` files (no `mcp` wrapper key).
 
 #### NPX
 
 ```json
 {
-  "mcp": {
   "servers": {
     "everything": {
       "command": "npx",
@@ -178,7 +181,6 @@ Optionally, you can add it to a file called `.vscode/mcp.json` in your workspace
     }
   }
 }
-}
 ```
 
 ## Running from source with [HTTP+SSE Transport](https://modelcontextprotocol.io/specification/2024-11-05/basic/transports#http-with-sse) (deprecated as of [2025-03-26](https://modelcontextprotocol.io/specification/2025-03-26/basic/transports))

src/filesystem/README.md

@@ -201,11 +201,15 @@ For quick installation, click the installation buttons below...
 
 [![Install with Docker in VS Code](https://img.shields.io/badge/VS_Code-Docker-0098FF?style=flat-square&logo=visualstudiocode&logoColor=white)](https://insiders.vscode.dev/redirect/mcp/install?name=filesystem&config=%7B%22command%22%3A%22docker%22%2C%22args%22%3A%5B%22run%22%2C%22-i%22%2C%22--rm%22%2C%22--mount%22%2C%22type%3Dbind%2Csrc%3D%24%7BworkspaceFolder%7D%2Cdst%3D%2Fprojects%2Fworkspace%22%2C%22mcp%2Ffilesystem%22%2C%22%2Fprojects%22%5D%7D) [![Install with Docker in VS Code Insiders](https://img.shields.io/badge/VS_Code_Insiders-Docker-24bfa5?style=flat-square&logo=visualstudiocode&logoColor=white)](https://insiders.vscode.dev/redirect/mcp/install?name=filesystem&config=%7B%22command%22%3A%22docker%22%2C%22args%22%3A%5B%22run%22%2C%22-i%22%2C%22--rm%22%2C%22--mount%22%2C%22type%3Dbind%2Csrc%3D%24%7BworkspaceFolder%7D%2Cdst%3D%2Fprojects%2Fworkspace%22%2C%22mcp%2Ffilesystem%22%2C%22%2Fprojects%22%5D%7D&quality=insiders)
 
-For manual installation, add the following JSON block to your User Settings (JSON) file in VS Code. You can do this by pressing `Ctrl + Shift + P` and typing `Preferences: Open Settings (JSON)`.
+For manual installation, you can configure the MCP server using one of these methods:
 
-Optionally, you can add it to a file called `.vscode/mcp.json` in your workspace. This will allow you to share the configuration with others.
+**Method 1: User Configuration (Recommended)**
+Add the configuration to your user-level MCP configuration file. Open the Command Palette (`Ctrl + Shift + P`) and run `MCP: Open User Configuration`. This will open your user `mcp.json` file where you can add the server configuration.
 
-> Note that the `mcp` key is not needed in the `.vscode/mcp.json` file.
+**Method 2: Workspace Configuration**
+Alternatively, you can add the configuration to a file called `.vscode/mcp.json` in your workspace. This will allow you to share the configuration with others.
+
+> Note that the `servers` object should be at the root level in `mcp.json` files (no `mcp` wrapper key).
 
 You can provide sandboxed directories to the server by mounting them to `/projects`. Adding the `ro` flag will make the directory readonly by the server.
 
@@ -214,7 +218,6 @@ Note: all directories must be mounted to `/projects` by default.
 
 ```json
 {
-  "mcp": {
   "servers": {
     "filesystem": {
       "command": "docker",
@@ -229,14 +232,12 @@ Note: all directories must be mounted to `/projects` by default.
     }
   }
 }
-}
 ```
 
 ### NPX
 
 ```json
 {
-  "mcp": {
   "servers": {
     "filesystem": {
       "command": "npx",
@@ -248,7 +249,6 @@ Note: all directories must be mounted to `/projects` by default.
     }
   }
 }
-}
 ```
 
 ## Build

src/git/README.md

@@ -173,15 +173,18 @@ For quick installation, use one of the one-click install buttons below...
 
 [![Install with Docker in VS Code](https://img.shields.io/badge/VS_Code-Docker-0098FF?style=flat-square&logo=visualstudiocode&logoColor=white)](https://insiders.vscode.dev/redirect/mcp/install?name=git&config=%7B%22command%22%3A%22docker%22%2C%22args%22%3A%5B%22run%22%2C%22--rm%22%2C%22-i%22%2C%22--mount%22%2C%22type%3Dbind%2Csrc%3D%24%7BworkspaceFolder%7D%2Cdst%3D%2Fworkspace%22%2C%22mcp%2Fgit%22%5D%7D) [![Install with Docker in VS Code Insiders](https://img.shields.io/badge/VS_Code_Insiders-Docker-24bfa5?style=flat-square&logo=visualstudiocode&logoColor=white)](https://insiders.vscode.dev/redirect/mcp/install?name=git&config=%7B%22command%22%3A%22docker%22%2C%22args%22%3A%5B%22run%22%2C%22--rm%22%2C%22-i%22%2C%22--mount%22%2C%22type%3Dbind%2Csrc%3D%24%7BworkspaceFolder%7D%2Cdst%3D%2Fworkspace%22%2C%22mcp%2Fgit%22%5D%7D&quality=insiders)
 
-For manual installation, add the following JSON block to your User Settings (JSON) file in VS Code. You can do this by pressing `Ctrl + Shift + P` and typing `Preferences: Open Settings (JSON)`.
+For manual installation, you can configure the MCP server using one of these methods:
 
-Optionally, you can add it to a file called `.vscode/mcp.json` in your workspace. This will allow you to share the configuration with others. 
+**Method 1: User Configuration (Recommended)**
+Add the configuration to your user-level MCP configuration file. Open the Command Palette (`Ctrl + Shift + P`) and run `MCP: Open User Configuration`. This will open your user `mcp.json` file where you can add the server configuration.
 
-> Note that the `mcp` key is not needed in the `.vscode/mcp.json` file.
+**Method 2: Workspace Configuration**
+Alternatively, you can add the configuration to a file called `.vscode/mcp.json` in your workspace. This will allow you to share the configuration with others.
+
+> Note that the `servers` object should be at the root level in `mcp.json` files (no `mcp` wrapper key).
 
 ```json
 {
-  "mcp": {
   "servers": {
     "git": {
       "command": "uvx",
@@ -189,7 +192,6 @@ Optionally, you can add it to a file called `.vscode/mcp.json` in your workspace
     }
   }
 }
-}
 ```
 
 For Docker installation:

src/memory/README.md

@@ -190,17 +190,20 @@ For quick installation, use one of the one-click installation buttons below:
 
 [![Install with Docker in VS Code](https://img.shields.io/badge/VS_Code-Docker-0098FF?style=flat-square&logo=visualstudiocode&logoColor=white)](https://insiders.vscode.dev/redirect/mcp/install?name=memory&config=%7B%22command%22%3A%22docker%22%2C%22args%22%3A%5B%22run%22%2C%22-i%22%2C%22-v%22%2C%22claude-memory%3A%2Fapp%2Fdist%22%2C%22--rm%22%2C%22mcp%2Fmemory%22%5D%7D) [![Install with Docker in VS Code Insiders](https://img.shields.io/badge/VS_Code_Insiders-Docker-24bfa5?style=flat-square&logo=visualstudiocode&logoColor=white)](https://insiders.vscode.dev/redirect/mcp/install?name=memory&config=%7B%22command%22%3A%22docker%22%2C%22args%22%3A%5B%22run%22%2C%22-i%22%2C%22-v%22%2C%22claude-memory%3A%2Fapp%2Fdist%22%2C%22--rm%22%2C%22mcp%2Fmemory%22%5D%7D&quality=insiders)
 
-For manual installation, add the following JSON block to your User Settings (JSON) file in VS Code. You can do this by pressing `Ctrl + Shift + P` and typing `Preferences: Open Settings (JSON)`.
+For manual installation, you can configure the MCP server using one of these methods:
 
-Optionally, you can add it to a file called `.vscode/mcp.json` in your workspace. This will allow you to share the configuration with others. 
+**Method 1: User Configuration (Recommended)**
+Add the configuration to your user-level MCP configuration file. Open the Command Palette (`Ctrl + Shift + P`) and run `MCP: Open User Configuration`. This will open your user `mcp.json` file where you can add the server configuration.
 
-> Note that the `mcp` key is not needed in the `.vscode/mcp.json` file.
+**Method 2: Workspace Configuration**
+Alternatively, you can add the configuration to a file called `.vscode/mcp.json` in your workspace. This will allow you to share the configuration with others.
+
+> Note that the `servers` object should be at the root level in `mcp.json` files (no `mcp` wrapper key).
 
 #### NPX
 
 ```json
 {
-  "mcp": {
   "servers": {
     "memory": {
       "command": "npx",
@@ -211,14 +214,12 @@ Optionally, you can add it to a file called `.vscode/mcp.json` in your workspace
     }
   }
 }
-}
 ```
 
 #### Docker
 
 ```json
 {
-  "mcp": {
   "servers": {
     "memory": {
       "command": "docker",
@@ -233,7 +234,6 @@ Optionally, you can add it to a file called `.vscode/mcp.json` in your workspace
     }
   }
 }
-}
 ```
 
 ### System Prompt

src/sequentialthinking/README.md

@@ -88,17 +88,20 @@ For quick installation, click one of the installation buttons below...
 
 [![Install with Docker in VS Code](https://img.shields.io/badge/VS_Code-Docker-0098FF?style=flat-square&logo=visualstudiocode&logoColor=white)](https://insiders.vscode.dev/redirect/mcp/install?name=sequentialthinking&config=%7B%22command%22%3A%22docker%22%2C%22args%22%3A%5B%22run%22%2C%22--rm%22%2C%22-i%22%2C%22mcp%2Fsequentialthinking%22%5D%7D) [![Install with Docker in VS Code Insiders](https://img.shields.io/badge/VS_Code_Insiders-Docker-24bfa5?style=flat-square&logo=visualstudiocode&logoColor=white)](https://insiders.vscode.dev/redirect/mcp/install?name=sequentialthinking&config=%7B%22command%22%3A%22docker%22%2C%22args%22%3A%5B%22run%22%2C%22--rm%22%2C%22-i%22%2C%22mcp%2Fsequentialthinking%22%5D%7D&quality=insiders)
 
-For manual installation, add the following JSON block to your User Settings (JSON) file in VS Code. You can do this by pressing `Ctrl + Shift + P` and typing `Preferences: Open Settings (JSON)`.
+For manual installation, you can configure the MCP server using one of these methods:
 
-Optionally, you can add it to a file called `.vscode/mcp.json` in your workspace. This will allow you to share the configuration with others.
+**Method 1: User Configuration (Recommended)**
+Add the configuration to your user-level MCP configuration file. Open the Command Palette (`Ctrl + Shift + P`) and run `MCP: Open User Configuration`. This will open your user `mcp.json` file where you can add the server configuration.
 
-> Note that the `mcp` key is not needed in the `.vscode/mcp.json` file.
+**Method 2: Workspace Configuration**
+Alternatively, you can add the configuration to a file called `.vscode/mcp.json` in your workspace. This will allow you to share the configuration with others.
+
+> Note that the `servers` object should be at the root level in `mcp.json` files (no `mcp` wrapper key).
 
 For NPX installation:
 
 ```json
 {
-  "mcp": {
   "servers": {
     "sequential-thinking": {
       "command": "npx",
@@ -109,14 +112,12 @@ For NPX installation:
     }
   }
 }
-}
 ```
 
 For Docker installation:
 
 ```json
 {
-  "mcp": {
   "servers": {
     "sequential-thinking": {
       "command": "docker",
@@ -129,7 +130,6 @@ For Docker installation:
     }
   }
 }
-}
 ```
 
 ## Building