NeuroNest User Guide — Complete 28-Section Reference

The comprehensive reference for NeuroNest covering every feature, panel, command, and configuration option. Whether you're getting started or tuning a complex multi-agent workflow, this guide has the answer.

Guide Contents (28 Sections)

1. Installation and Activation — downloading installers, running the setup wizard, and entering your PQC beta activation code
2. Interface Overview — the six main panels: Editor, Agent, Code Graph, Security Console, Terminal, and Output
3. Opening a Project — local directories, Git repository cloning, and multi-root workspaces
4. The Agent Panel — browsing all 117+ agents by department, filtering, and starting agent conversations
5. The ZERA Optimizer — how cross-agent task scheduling works, topology selection, and configuration
6. Code Graph Viewer — navigating the live semantic code graph, filtering by file type, and graph layouts
7. Running Your First Agent — step-by-step walkthrough of your first agent interaction
8. Multi-Agent Workflows — creating and configuring Sequential, Star, Hierarchy, Mesh, and Hybrid topologies
9. Agent Recipes — saving, naming, versioning, and sharing multi-agent workflow templates
10. Security Policy Settings — configuring the 7-layer policy engine for your environment
11. Prompt Injection Protection — understanding the dual-layer firewall and tuning sensitivity
12. Edit Lock System — marking files and directories as protected from agent modification
13. Local Inference Configuration — Ollama model management, llama.cpp setup, and GPU offload tuning
14. Cloud Model Providers — API key setup for OpenAI, Anthropic, Gemini, DeepSeek, Grok, Mistral, NVIDIA NIM, Groq
15. Git Integration — commit, branch, PR creation, and merge with agent assistance
16. CI/CD Integration — connecting GitHub Actions, GitLab CI, Jenkins, and CircleCI
17. Terminal Integration — using the built-in terminal alongside agent workflows
18. Plugin Management — installing, configuring, and building SDK plugins
19. Knowledge Graph Configuration — tree-sitter language support, graph update frequency, and layout settings
20. Agent Memory Management — context window sizes, persistent memory, and memory pruning strategies
21. Debugging Agent Actions — the Action Log, action replay, and rollback functionality
22. Performance Tuning — GPU offload configuration, model quantization, context length optimization
23. Team Collaboration — session sharing, co-editing, and shared Agent Recipe libraries
24. License and Activation Management — transferring activations, team licenses, and managing multiple machines
25. Telemetry and Privacy — what is collected, what stays local, crash reporting, and opt-out
26. Keyboard Shortcuts — complete reference for all keyboard shortcuts across all panels
27. Troubleshooting — error codes, diagnostic commands, log locations, and common solutions
28. Changelog — version history and full release notes for all NeuroNest versions