enhance docs structure (#155)

eleonorecharles · web-flow · commit 859e19dfeb92 · 2025-10-31T07:13:50.000-07:00
diff --git a/docs/docs/clients/_category_.yaml b/docs/docs/clients/_category_.yaml
@@ -1,2 +1,2 @@
 label: "Clients"
-position: 4
+position: 6
diff --git a/docs/docs/clients/claude_desktop/index.mdx b/docs/docs/clients/claude_desktop/index.mdx
@@ -19,7 +19,7 @@ NIXPKGS_ALLOW_UNFREE=1 nix run github:k3d3/claude-desktop-linux-flake \
 
 ## Configure Jupyter MCP Server
 
-To use Jupyter MCP Server with Claude Desktop, add the [Jupyter MCP Server configuration](/deployment/jupyter/stdio#2-setup-jupyter-mcp-server) to your `claude_desktop_config.json` file, read more on the [MCP documentation website](https://modelcontextprotocol.io/quickstart/user#2-add-the-filesystem-mcp-server).
+To use Jupyter MCP Server with Claude Desktop, add the [Jupyter MCP Server configuration](/jupyter/stdio#2-setup-jupyter-mcp-server) to your `claude_desktop_config.json` file, read more on the [MCP documentation website](https://modelcontextprotocol.io/quickstart/user#2-add-the-filesystem-mcp-server).
 
 **📺 Watch the setup demo**
 
diff --git a/docs/docs/clients/cline/index.mdx b/docs/docs/clients/cline/index.mdx
@@ -8,4 +8,4 @@ Install the Cline VS Code extension from the [VS Code Marketplace](https://marke
 
 ## Configure Jupyter MCP Server
 
-To use Jupyter MCP Server with Cline, add the [Jupyter MCP Server configuration](/deployment/jupyter/stdio#2-setup-jupyter-mcp-server) to your `.cline_mcp_settings.json` file, read more on the [Cline documentation](https://marketplace.visualstudio.com/items?itemName=saoudrizwan.claude-dev).
+To use Jupyter MCP Server with Cline, add the [Jupyter MCP Server configuration](/jupyter/stdio#2-setup-jupyter-mcp-server) to your `.cline_mcp_settings.json` file, read more on the [Cline documentation](https://marketplace.visualstudio.com/items?itemName=saoudrizwan.claude-dev).
diff --git a/docs/docs/clients/cursor/index.mdx b/docs/docs/clients/cursor/index.mdx
@@ -8,4 +8,4 @@ Install the Cursor app from the [Cursor website](https://www.cursor.com/download
 
 ## Configure Jupyter MCP Server
 
-To use Jupyter MCP Server with Cursor, add the [Jupyter MCP Server configuration](/deployment/jupyter/stdio#2-setup-jupyter-mcp-server) to your `.cursor/mcp.json` file, read more on the [MCP Cursor documentation website](https://docs.cursor.com/context/model-context-protocol#configuring-mcp-servers).
+To use Jupyter MCP Server with Cursor, add the [Jupyter MCP Server configuration](/jupyter/stdio#2-setup-jupyter-mcp-server) to your `.cursor/mcp.json` file, read more on the [MCP Cursor documentation website](https://docs.cursor.com/context/model-context-protocol#configuring-mcp-servers).
diff --git a/docs/docs/clients/vscode/index.mdx b/docs/docs/clients/vscode/index.mdx
@@ -106,7 +106,7 @@ For advanced deployments with separate document and runtime servers:
 
 </details>
 
-Update with the actual configuration details from the [Jupyter MCP Server configuration](/deployment/jupyter/stdio#2-setup-jupyter-mcp-server).
+Update with the actual configuration details from the [Jupyter MCP Server configuration](/jupyter/stdio#2-setup-jupyter-mcp-server).
 
 ###  As Workspace Settings in `.vscode/mcp.json`
 
@@ -186,7 +186,7 @@ For advanced deployments with separate document and runtime servers:
 
 </details>
 
-Update with the actual configuration details from the [Jupyter MCP Server configuration](/deployment/jupyter/stdio#2-setup-jupyter-mcp-server).
+Update with the actual configuration details from the [Jupyter MCP Server configuration](/jupyter/stdio#2-setup-jupyter-mcp-server).
 
 This enables workspace-specific configuration and sharing.
 
diff --git a/docs/docs/clients/windsurf/index.mdx b/docs/docs/clients/windsurf/index.mdx
@@ -8,4 +8,4 @@ Install the Windsurf app from the [Windsurf website](https://windsurf.com/downlo
 
 ## Configure Jupyter MCP Server
 
-To use Jupyter MCP Server with Windsurf, add the [Jupyter MCP Server configuration](/deployment/jupyter/stdio#2-setup-jupyter-mcp-server) to your `mcp_config.json` file, read more on the [MCP Windsurf documentation website](https://docs.windsurf.com/windsurf/cascade/mcp).
+To use Jupyter MCP Server with Windsurf, add the [Jupyter MCP Server configuration](/jupyter/stdio#2-setup-jupyter-mcp-server) to your `mcp_config.json` file, read more on the [MCP Windsurf documentation website](https://docs.windsurf.com/windsurf/cascade/mcp).
diff --git a/docs/docs/configuration/_category_.yaml b/docs/docs/configuration/_category_.yaml
@@ -0,0 +1,2 @@
+label: "Configuration"
+position: 5
diff --git a/docs/docs/configuration/index.mdx b/docs/docs/configuration/index.mdx
@@ -1,4 +1,4 @@
-# Server Configuration
+# Configuration
 
 ## Overview
 
diff --git a/docs/docs/configure/_category_.yaml b/docs/docs/configure/_category_.yaml
diff --git a/docs/docs/datalayer/_category_.yaml b/docs/docs/datalayer/_category_.yaml
@@ -1,2 +1,2 @@
 label: "Datalayer Notebooks"
-position: 2
+position: 4
diff --git a/docs/docs/datalayer/streamable-http/index.mdx b/docs/docs/datalayer/streamable-http/index.mdx
diff --git a/docs/docs/deployment/_category_.yaml b/docs/docs/deployment/_category_.yaml
diff --git a/docs/docs/getting_started/_category_.yaml b/docs/docs/getting_started/_category_.yaml
@@ -0,0 +1,2 @@
+label: "Getting Started"
+position: 2
diff --git a/docs/docs/getting_started/index.mdx b/docs/docs/getting_started/index.mdx
@@ -1,6 +1,6 @@
-# Deployment
+# Getting Started 
 
-Jupyter MCP Server can be deployed in various configurations depending on your needs. It can be running inside the Jupyter Server **as a Jupyter Server Extension**, or as a **Standalone Server** connecting to a **local or remote Jupyter server** or to [**Datalayer**](https://datalayer.ai) hosted Notebooks.
+Jupyter MCP Server can be started in various configurations depending on your needs. It can be running inside the Jupyter Server **as a Jupyter Server Extension**, or as a **Standalone Server** connecting to a **local or remote Jupyter server** or to [**Datalayer**](https://datalayer.ai) hosted Notebooks.
 
 Navigate to the relevant section based on your needs:
 - ***Jupyter Notebooks***: If you want to interact with notebooks in JupyterLab/JupyterHub.
diff --git a/docs/docs/index.mdx b/docs/docs/index.mdx
@@ -34,7 +34,7 @@ To use Jupyter MCP Server, you first need to decide which setup fits your needs:
 - ***MCP Transport***: Do you want to set up the MCP Server using standard input/output (STDIO) transport or Streamable HTTP transport?
 - ***MCP Server Location***: Do you want to set up the MCP Server as a Standalone Server or as a Jupyter Server Extension?
 
-Navigate to the relevant section in the [Deployment](./deployment) page to get started based on your needs.
+Navigate to the relevant section in the [Getting Started](./getting_started) page to get started based on your needs.
 
 Looking for blog posts, videos or other resources related to Jupyter MCP Server?  <br />
 👉 Check out the [Resources](./resources) section.
diff --git a/docs/docs/jupyter/_category_.yaml b/docs/docs/jupyter/_category_.yaml
@@ -1,2 +1,2 @@
 label: "Jupyter Notebooks"
-position: 1
+position: 3
diff --git a/docs/docs/jupyter/index.mdx b/docs/docs/jupyter/index.mdx
@@ -4,11 +4,11 @@
 This guide will help you set up a Jupyter MCP Server to connect your preferred MCP client to a JupyterLab instance.
 The Jupyter MCP Server acts as a bridge between the MCP client and the JupyterLab server, allowing you to interact with Jupyter notebooks seamlessly.
 
-You can customize the setup further based on your requirements. Refer to the [server configuration](/configure) for more details on the possible configurations.
+You can customize the setup further based on your requirements. Refer to the [server configuration](/configuration) for more details on the possible configurations.
 
 :::tip JupyterLab Mode
 
-**New in v0.17.0**: Enable JupyterLab mode for enhanced UI integration! When enabled, notebooks automatically open in JupyterLab and additional UI tools become available. See the [JupyterLab Mode configuration](/configure#jupyterlab-mode) for details.
+**New in v0.17.0**: Enable JupyterLab mode for enhanced UI integration! When enabled, notebooks automatically open in JupyterLab and additional UI tools become available. See the [JupyterLab Mode configuration](/configuration#jupyterlab-mode) for details.
 
 :::
 
diff --git a/docs/docs/jupyter/stdio/_category_.yaml b/docs/docs/jupyter/stdio/_category_.yaml
diff --git a/docs/docs/jupyter/stdio/index.mdx b/docs/docs/jupyter/stdio/index.mdx
@@ -41,7 +41,7 @@ Choose your deployment method: **uvx** (lightweight, recommended for first try)
 :::important
 **Before You Start:**
 - Ensure the port in your configuration matches your `jupyter lab` command port
-- See the [server configuration guide](/configure) for all available options and detailed examples
+- See the [server configuration guide](/configuration) for all available options and detailed examples
 :::
 
 ### Using UVX (Quick Start)
@@ -98,7 +98,7 @@ For deployments requiring separate document storage and runtime execution:
 
 ### Using Docker (Production)
 
-Configuration varies by operating system. For complete configuration options, see the [server configuration guide](/configure).
+Configuration varies by operating system. For complete configuration options, see the [server configuration guide](/configuration).
 
 #### For MacOS and Windows
 
@@ -222,7 +222,7 @@ For deployments requiring separate document storage and runtime execution:
 
 </details>
 
-For advanced configurations with separate document storage and runtime execution, see the [complete configuration examples](/configure#configuration-examples).
+For advanced configurations with separate document storage and runtime execution, see the [complete configuration examples](/configuration#configuration-examples).
 
 ## Troubleshooting
 
@@ -238,4 +238,4 @@ For advanced configurations with separate document storage and runtime execution
 - Test token: `curl -H "Authorization: token YOUR_TOKEN" http://localhost:8888/api/sessions`
 - Check token in Jupyter server logs or URL parameters
 
-For detailed troubleshooting and advanced configuration, see the [configuration guide](/configure).
+For detailed troubleshooting and advanced configuration, see the [configuration guide](/configuration).
diff --git a/docs/docs/jupyter/streamable-http/_category_.yaml b/docs/docs/jupyter/streamable-http/_category_.yaml
diff --git a/docs/docs/jupyter/streamable-http/jupyter-extension/index.mdx b/docs/docs/jupyter/streamable-http/jupyter-extension/index.mdx
@@ -17,18 +17,12 @@ pip install datalayer_pycrdt==0.12.17 jupyter_mcp_tools
 Start JupyterLab with the MCP server extension:
 
 ```bash
-jupyter lab \
-  --JupyterMCPServerExtensionApp.document_url local \
-  --JupyterMCPServerExtensionApp.runtime_url local \
-  --JupyterMCPServerExtensionApp.start_new_runtime True \
-  --ServerApp.disable_check_xsrf True \
-  --IdentityProvider.token MY_TOKEN \
-  --port 4040
+jupyter lab --port 4040
 ```
 
 This starts JupyterLab at [http://127.0.0.1:4040](http://127.0.0.1:4040) with the MCP server integrated.
 
-For complete configuration options, see the [server configuration guide](/configure).
+For complete configuration options, see the [server configuration guide](/configuration).
 
 ## 2. Configure your MCP Client
 
@@ -57,4 +51,4 @@ Use the following configuration to connect to the integrated MCP server:
 - Verify server is running at: `curl http://localhost:4040/mcp`
 - Check that port 4040 is not blocked
 
-For detailed configuration and troubleshooting, see the [configuration guide](/configure).
+For detailed configuration and troubleshooting, see the [configuration guide](/configuration).
diff --git a/docs/docs/jupyter/streamable-http/standalone/index.mdx b/docs/docs/jupyter/streamable-http/standalone/index.mdx
@@ -34,7 +34,7 @@ For JupyterHub:
 - Ensure your API token (`MY_TOKEN`) is created with `access:servers` scope in the Hub.
 :::
 
-## 2. Setup Jupyter MCP Server
+## 2. Start Jupyter MCP Server
 
 The server runs on port `4040` and provides a streamable HTTP endpoint at `http://localhost:4040/mcp`.
 
@@ -74,7 +74,7 @@ docker run \
   --transport streamable-http
 ```
 
-For advanced configuration options, see the [server configuration guide](/configure).
+For advanced configuration options, see the [server configuration guide](/configuration).
 
 <!--
 
@@ -116,4 +116,4 @@ Use the following configuration to connect to the running server:
 - Verify `JUPYTER_TOKEN` matches your Jupyter server token
 - Check Jupyter server is accessible from MCP server
 
-For detailed configuration and troubleshooting, see the [configuration guide](/configure).
+For detailed configuration and troubleshooting, see the [configuration guide](/configuration).
diff --git a/docs/docs/releases/index.mdx b/docs/docs/releases/index.mdx
@@ -57,4 +57,4 @@ See the latest release notes on the [GitHub Releases page](https://github.com/da
 
 ### 0.6.0 - 01 Jul 2025
 
-- Configuration change, see details on the [clients page](/clients) and [server configuration](/configure).
+- Configuration change, see details on the [clients page](/clients) and [server configuration](/configuration).
diff --git a/docs/docs/tools/_category_.yaml b/docs/docs/tools/_category_.yaml
@@ -1,2 +1,2 @@
 label: "Tools"
-position: 8
+position: 5

Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`	`1`	`label: "Clients"`
`2`		`-position: 4`
	`2`	`+position: 6`
Original file line number	Diff line number	Diff line change
`@@ -8,4 +8,4 @@ Install the Cline VS Code extension from the [VS Code Marketplace](https://marke`
`8`	`8`
`9`	`9`	`## Configure Jupyter MCP Server`
`10`	`10`
`11`		-To use Jupyter MCP Server with Cline, add the [Jupyter MCP Server configuration](/deployment/jupyter/stdio#2-setup-jupyter-mcp-server) to your `.cline_mcp_settings.json` file, read more on the [Cline documentation](https://marketplace.visualstudio.com/items?itemName=saoudrizwan.claude-dev).
	`11`	+To use Jupyter MCP Server with Cline, add the [Jupyter MCP Server configuration](/jupyter/stdio#2-setup-jupyter-mcp-server) to your `.cline_mcp_settings.json` file, read more on the [Cline documentation](https://marketplace.visualstudio.com/items?itemName=saoudrizwan.claude-dev).
Original file line number	Diff line number	Diff line change
`@@ -8,4 +8,4 @@ Install the Cursor app from the [Cursor website](https://www.cursor.com/download`
`8`	`8`
`9`	`9`	`## Configure Jupyter MCP Server`
`10`	`10`
`11`		-To use Jupyter MCP Server with Cursor, add the [Jupyter MCP Server configuration](/deployment/jupyter/stdio#2-setup-jupyter-mcp-server) to your `.cursor/mcp.json` file, read more on the [MCP Cursor documentation website](https://docs.cursor.com/context/model-context-protocol#configuring-mcp-servers).
	`11`	+To use Jupyter MCP Server with Cursor, add the [Jupyter MCP Server configuration](/jupyter/stdio#2-setup-jupyter-mcp-server) to your `.cursor/mcp.json` file, read more on the [MCP Cursor documentation website](https://docs.cursor.com/context/model-context-protocol#configuring-mcp-servers).
Original file line number	Diff line number	Diff line change
`@@ -8,4 +8,4 @@ Install the Windsurf app from the [Windsurf website](https://windsurf.com/downlo`
`8`	`8`
`9`	`9`	`## Configure Jupyter MCP Server`
`10`	`10`
`11`		-To use Jupyter MCP Server with Windsurf, add the [Jupyter MCP Server configuration](/deployment/jupyter/stdio#2-setup-jupyter-mcp-server) to your `mcp_config.json` file, read more on the [MCP Windsurf documentation website](https://docs.windsurf.com/windsurf/cascade/mcp).
	`11`	+To use Jupyter MCP Server with Windsurf, add the [Jupyter MCP Server configuration](/jupyter/stdio#2-setup-jupyter-mcp-server) to your `mcp_config.json` file, read more on the [MCP Windsurf documentation website](https://docs.windsurf.com/windsurf/cascade/mcp).
Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+label: "Configuration"`
	`2`	`+position: 5`
Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-# Server Configuration`
	`1`	`+# Configuration`
`2`	`2`
`3`	`3`	`## Overview`
`4`	`4`
Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`	`1`	`label: "Datalayer Notebooks"`
`2`		`-position: 2`
	`2`	`+position: 4`