Rebuild documentation site from scratch with Docusaurus 3.9.2

Fresh Docusaurus 3 project replacing the hacked-together extraction from
the old iowarp.github.io repo. Key changes:

- Clean Docusaurus 3.9.2 scaffold with TypeScript
- IOWarp brand theme (teal/orange/cream) consistent with toolkit.iowarp.ai
- Neobrutalist design accents on nav/footer, clean readable doc content
- Beautiful landing page with section cards at docs.iowarp.ai root
- Restructured docs: getting-started, clio-kit, sdk, api, deployment, faq
- Proper frontmatter with descriptions on all pages
- Tabs for installation methods (Docker/Native/Spack)
- Tabs for IDE integration (Cursor/Claude Code/VS Code/Claude Desktop)
- Removed 80+ unused static images (papers, demos, logos)
- Clean MCP servers reference page with summary tables
- GitHub Actions deploy workflow for GitHub Pages
- robots.txt, llms.txt, CNAME for docs.iowarp.ai
- Zero build warnings, zero broken links

Co-authored-by: Cursor <cursoragent@cursor.com>

Author: akougkas

.gitignore

@@ -18,18 +18,3 @@
 npm-debug.log*
 yarn-debug.log*
 yarn-error.log*
-
-.playwright-mcp
-
-.specify
-.cursor
-.husky
-.lintstagedrc
-.claude
-specs/
-.windsurf/
-
-vision-sources/
-
-# Archived shadow pages (not compiled, content preserved locally)
-src/pages/_archived/

LICENSE

@@ -1,43 +1,47 @@
 # IOWarp Documentation
 
-Technical documentation for the [IOWarp](https://iowarp.ai) context engineering platform.
+Technical documentation for the [IOWarp](https://iowarp.ai) context orchestration platform, served at **[docs.iowarp.ai](https://docs.iowarp.ai)**.
 
-**Live site**: [docs.iowarp.ai](https://docs.iowarp.ai)
+Built with [Docusaurus 3](https://docusaurus.io/) and deployed via GitHub Pages.
 
 ## Development
 
 ```bash
 # Install dependencies
 npm install
 
-# Start dev server
+# Start dev server (http://localhost:4000)
 npm start
 
 # Build for production
 npm run build
+
+# Serve production build locally
+npm run serve
 ```
 
 ## Structure
 
 ```
-docs/                          # Documentation markdown files
-  getting-started/             # Installation and quick start
-  deployment/                  # HPC cluster deployment
-  agent-toolkit/               # CLIO Kit MCP servers
-  sdk/                         # IOWarp SDK (Hermes, Chimaera, CLIO Transfer)
-  api/                         # Python and Storage API reference
-  faq/                         # Troubleshooting
-static/                        # Static assets
-docusaurus.config.ts           # Site configuration
-sidebars.ts                    # Sidebar navigation
+docs/
+├── intro.md                  # Welcome & overview
+├── getting-started/          # Installation, quick start
+├── clio-kit/                 # MCP servers reference
+├── sdk/                      # IPC, runtime modules, CTE, CAE
+├── api/                      # Python API, agent API, storage API
+├── deployment/               # Configuration, HPC, performance
+├── faq.md                    # FAQ & troubleshooting
+└── tutorials.md              # Step-by-step guides
 ```
 
 ## Related Sites
 
-- [iowarp.ai](https://iowarp.ai) — Main project website (Astro)
-- [toolkit.iowarp.ai](https://toolkit.iowarp.ai) — CLIO Kit MCP server showcase (Docusaurus)
-- [docs.iowarp.ai](https://docs.iowarp.ai) — This site (Docusaurus)
+| Site | URL | Repository |
+|------|-----|-----------|
+| IOWarp Website | [iowarp.ai](https://iowarp.ai) | [iowarp/iowarp.github.io](https://github.com/iowarp/iowarp.github.io) |
+| CLIO Kit Showcase | [toolkit.iowarp.ai](https://toolkit.iowarp.ai) | [iowarp/clio-kit](https://github.com/iowarp/clio-kit) |
+| Documentation | [docs.iowarp.ai](https://docs.iowarp.ai) | [iowarp/docs](https://github.com/iowarp/docs) |
 
 ## License
 
-BSD 3-Clause License. See [LICENSE](LICENSE).
+BSD 3-Clause — [Gnosis Research Center](https://grc.iit.edu/), Illinois Institute of Technology

README.md

@@ -1,3 +1,30 @@
+---
+sidebar_position: 2
+title: Agent API
+description: API reference for integrating AI agents with the IOWarp runtime.
+---
+
 # Agent API
 
-*Coming soon*
+:::info Coming Soon
+The Agent API documentation is being developed. This will cover:
+
+- **CLIO Agent SDK** — Programmatic agent orchestration
+- **Context Engineering API** — Building custom context pipelines
+- **Workflow Definitions** — Declarative scientific workflow specifications
+- **Event System** — Subscribe to runtime events and telemetry
+:::
+
+## Current Integration Points
+
+AI agents currently interact with IOWarp through:
+
+1. **CLIO Kit MCP Servers** — 16 servers with 150+ tools via the [Model Context Protocol](../clio-kit/mcp-servers)
+2. **Python API** — Direct runtime interaction via the [Python bindings](./python)
+3. **CLI Tools** — Command-line utilities for runtime management
+
+## Resources
+
+- [CLIO Agent Overview](https://iowarp.ai/platform/clio-agent/) — Architecture and design
+- [CLIO Kit](https://toolkit.iowarp.ai) — Interactive MCP server showcase
+- [GitHub Issues](https://github.com/iowarp/iowarp/issues) — Request API features

docs/agent-toolkit/mcp.md

@@ -1,4 +1,10 @@
-# Context Exploration Engine - Python API Documentation
+---
+sidebar_position: 1
+title: Python API
+description: Python API reference for the Context Exploration Engine (CEE) — data assimilation, querying, and retrieval.
+---
+
+# Python API — Context Exploration Engine (CEE)
 
 ## Overview
 

docs/api/agents.md

@@ -1,3 +1,32 @@
+---
+sidebar_position: 3
+title: Storage API
+description: API reference for the IOWarp storage layer and Context Transfer Engine.
+---
+
 # Storage API
 
-*Coming soon*
+:::info Coming Soon
+The Storage API documentation is being developed. This will cover:
+
+- **CTE Client API** — Blob Put/Get/Delete operations
+- **Multi-Tier Storage** — Programmatic tier management
+- **Data Placement Engine** — Custom placement policies
+- **Streaming API** — Chunked reads/writes for large datasets
+:::
+
+## Current Access Methods
+
+Storage operations are currently available through:
+
+1. **Python API** — High-level blob operations via [Python bindings](./python)
+2. **C++ SDK** — Native CTE client for high-performance applications (see [Context Transfer Engine](../sdk/context-transfer))
+3. **Docker Runtime** — Container-based deployment with YAML configuration (see [Configuration](../deployment/configuration))
+
+## Configuration
+
+Storage tiers are configured in `wrp_conf.yaml`. See the [Configuration Reference](../deployment/configuration) for details on:
+
+- RAM, NVMe, SSD, and HDD tier setup
+- Data placement engine (`max_bw`, `round_robin`, `random`)
+- Capacity limits and scoring

docs/api/python-api.md docs/api/python.mddocs/api/python-api.md renamed to docs/api/python.md

@@ -0,0 +1,167 @@
+---
+sidebar_position: 1
+title: MCP Servers
+description: "16 specialized Model Context Protocol servers for scientific computing — 150+ tools for HDF5, Slurm, ParaView, ArXiv, and more."
+---
+
+# CLIO Kit — MCP Servers
+
+**16 specialized MCP servers for scientific computing — 150+ tools**
+
+CLIO Kit provides AI agents with direct access to HPC infrastructure, scientific data formats, and research workflows through [Model Context Protocol](https://modelcontextprotocol.io/) (MCP) servers.
+
+:::tip
+For the interactive MCP showcase, visit [toolkit.iowarp.ai](https://toolkit.iowarp.ai).
+:::
+
+## Quick Start
+
+```bash
+# Install and run any MCP server
+uvx iowarp-agent-toolkit mcp-server hdf5
+uvx iowarp-agent-toolkit mcp-server pandas
+uvx iowarp-agent-toolkit mcp-server slurm
+
+# List all available servers
+uvx iowarp-agent-toolkit mcp-servers
+```
+
+## Available Servers
+
+### Data I/O & Visualization (5 servers, 56+ tools)
+
+| Server | Tools | Description |
+|--------|-------|-------------|
+| **HDF5** | 27 | HDF5 file operations with AI-powered insights, LRU caching, streaming |
+| **Pandas** | 15 | CSV data analysis, statistical summaries, data cleaning |
+| **ADIOS** | 5 | Scientific data I/O for BP5 format |
+| **Parquet** | 4 | High-performance columnar data processing |
+| **ParaView** | 29 | 3D scientific visualization, isosurfaces, streamlines |
+
+### HPC Integration (4 servers, 59+ tools)
+
+| Server | Tools | Description |
+|--------|-------|-------------|
+| **Slurm** | 13 | Job submission, monitoring, cluster analytics |
+| **Jarvis** | 25+ | HPC workflow orchestration, pipeline management |
+| **Lmod** | 10 | HPC module system management |
+| **Node Hardware** | 11 | CPU, GPU, memory, disk, network monitoring |
+
+### Research Discovery (2 servers, 16+ tools)
+
+| Server | Tools | Description |
+|--------|-------|-------------|
+| **ArXiv** | 13 | Paper search, metadata, BibTeX export, citation networks |
+| **NDP** | 3 | National Data Platform dataset discovery |
+
+### System Monitoring (2 servers, 14+ tools)
+
+| Server | Tools | Description |
+|--------|-------|-------------|
+| **Darshan** | 10 | I/O performance analysis, bandwidth, bottleneck detection |
+| **ChronoLog** | 4 | Session logging and context sharing |
+
+### Utilities (3 servers, 20+ tools)
+
+| Server | Tools | Description |
+|--------|-------|-------------|
+| **Plot** | 6 | Data visualization (line, bar, scatter, heatmap) |
+| **Compression** | 1 | File compression utilities |
+| **Parallel Sort** | 13 | Log processing, pattern detection, filtering |
+
+## IDE Integration
+
+import Tabs from '@theme/Tabs';
+import TabItem from '@theme/TabItem';
+
+<Tabs>
+<TabItem value="cursor" label="Cursor" default>
+
+Add to `~/.cursor/mcp.json`:
+
+```json
+{
+  "mcpServers": {
+    "hdf5-mcp": {
+      "command": "uvx",
+      "args": ["iowarp-agent-toolkit", "mcp-server", "hdf5"]
+    },
+    "pandas-mcp": {
+      "command": "uvx",
+      "args": ["iowarp-agent-toolkit", "mcp-server", "pandas"]
+    },
+    "slurm-mcp": {
+      "command": "uvx",
+      "args": ["iowarp-agent-toolkit", "mcp-server", "slurm"]
+    }
+  }
+}
+```
+
+[Cursor MCP docs →](https://docs.cursor.com/context/model-context-protocol)
+
+</TabItem>
+<TabItem value="claude-code" label="Claude Code">
+
+```bash
+claude mcp add hdf5-mcp -- uvx iowarp-agent-toolkit mcp-server hdf5
+claude mcp add pandas-mcp -- uvx iowarp-agent-toolkit mcp-server pandas
+claude mcp add slurm-mcp -- uvx iowarp-agent-toolkit mcp-server slurm
+```
+
+[Claude Code MCP docs →](https://code.claude.com/docs/en/mcp)
+
+</TabItem>
+<TabItem value="vscode" label="VS Code">
+
+Add to your VS Code MCP config:
+
+```json
+"mcp": {
+  "servers": {
+    "hdf5-mcp": {
+      "type": "stdio",
+      "command": "uvx",
+      "args": ["iowarp-agent-toolkit", "mcp-server", "hdf5"]
+    },
+    "pandas-mcp": {
+      "type": "stdio",
+      "command": "uvx",
+      "args": ["iowarp-agent-toolkit", "mcp-server", "pandas"]
+    }
+  }
+}
+```
+
+[VS Code MCP docs →](https://code.visualstudio.com/docs/copilot/chat/mcp-servers)
+
+</TabItem>
+<TabItem value="claude-desktop" label="Claude Desktop">
+
+Edit `claude_desktop_config.json`:
+
+```json
+{
+  "mcpServers": {
+    "hdf5-mcp": {
+      "command": "uvx",
+      "args": ["iowarp-agent-toolkit", "mcp-server", "hdf5"]
+    },
+    "arxiv-mcp": {
+      "command": "uvx",
+      "args": ["iowarp-agent-toolkit", "mcp-server", "arxiv"]
+    }
+  }
+}
+```
+
+[Claude Desktop MCP docs →](https://modelcontextprotocol.io/quickstart/user)
+
+</TabItem>
+</Tabs>
+
+## Repository
+
+- **GitHub**: [github.com/iowarp/clio-kit](https://github.com/iowarp/clio-kit)
+- **PyPI**: [pypi.org/project/clio-kit](https://pypi.org/project/clio-kit/)
+- **Interactive Showcase**: [toolkit.iowarp.ai](https://toolkit.iowarp.ai)

docs/api/storage.md

@@ -1,3 +1,9 @@
+---
+sidebar_position: 1
+title: Configuration
+description: Complete configuration reference for IOWarp runtime and CTE deployments.
+---
+
 # Configuration Reference
 
 This document describes how to configure IOWarp deployments.

docs/clio-kit/mcp-servers.md

@@ -1,3 +1,9 @@
+---
+sidebar_position: 2
+title: HPC Cluster
+description: Deploying IOWarp on HPC clusters with Spack and containers.
+---
+
 # HPC Cluster Deployment
 
 ## Spack (Manual)