Structure research project

CLAUDE.md

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+- Your research directory is `research`.
+- Keep track of researched features in @research/index.md.
+  - As you document each feature, update its status in the index.
+  - For each each feature, document these three things:
+    1. A short summary.
+    2. An in-depth technical description of systems and plausible reasons for their design.
+    3. A reference of classes/functions/methods.
+- Use `nix-shell` to grab temporary tools as needed.

research/index.md

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+# MatterControl Codebase Research Index
+
+This directory contains comprehensive documentation of the MatterControl 3D printing application codebase.
+
+## Project Overview
+
+**MatterControl** is a sophisticated 3D printing control application built in C# targeting .NET 6.0. It provides comprehensive 3D printing workflow management including model viewing, slicing, printer control, and print management.
+
+### Technology Stack
+- **Language:** C# (.NET 6.0)
+- **UI Framework:** agg-sharp (custom 2D/3D rendering engine)
+- **Database:** SQLite
+- **3D Rendering:** OpenGL
+- **Slicing Engine:** MatterSlice (internal)
+
+### Project Structure
+- **Total C# Files:** ~965
+- **Solution Projects:** 17
+- **Printer Profiles:** 56+
+
+---
+
+## Documentation Status
+
+| Document | Status | Last Updated |
+|----------|--------|--------------|
+| [Core Architecture](./01-core-architecture.md) | Pending | - |
+| [Application Controller](./02-application-controller.md) | Pending | - |
+| [UI & Rendering System](./03-ui-rendering.md) | Pending | - |
+| [3D View & Part Preview](./04-part-preview.md) | Pending | - |
+| [Printer Communication](./05-printer-communication.md) | Pending | - |
+| [Slicing System](./06-slicing-system.md) | Pending | - |
+| [Library & Content Management](./07-library-system.md) | Pending | - |
+| [Data Storage & Persistence](./08-data-storage.md) | Pending | - |
+| [Settings Management](./09-settings-management.md) | Pending | - |
+| [Design Tools](./10-design-tools.md) | Pending | - |
+| [Print Queue & History](./11-print-queue.md) | Pending | - |
+| [Plugin System](./12-plugin-system.md) | Pending | - |
+| [Mesh Operations](./13-mesh-operations.md) | Pending | - |
+| [Utilities & Helpers](./14-utilities.md) | Pending | - |
+
+---
+
+## Quick Reference
+
+### Main Entry Points
+- `Program.cs` - Application entry point
+- `MatterControlLib/ApplicationView/ApplicationController.cs` - Central controller
+- `MatterControlLib/ApplicationView/RootSystemWindow.cs` - Main window
+
+### Key Namespaces
+- `MatterHackers.MatterControl` - Main application
+- `MatterHackers.MatterControl.PrinterCommunication` - Printer drivers
+- `MatterHackers.MatterControl.SlicerConfiguration` - Slicing settings
+- `MatterHackers.MatterControl.PartPreviewWindow` - 3D visualization
+- `MatterHackers.MatterControl.Library` - Content management
+- `MatterHackers.MatterControl.DataStorage` - Database layer
+- `MatterHackers.MatterControl.DesignTools` - 3D editing tools