Remove repository clutter: legacy JSmol demos, sample data, stale docs

.github/copilot-instructions.md

@@ -13,11 +13,6 @@ jlmol is an Electron-based desktop application for molecular visualization built
   ```
   Takes ~5-25 seconds. Dependencies include electron, electron-builder, and various utilities.
 
-- Verify version management system:
-  ```bash
-  npm run check-version
-  ```
-  This ensures all files use dynamic version loading from package.json.
 
 ### Development and Testing
 - Run the application in development mode:
@@ -38,10 +33,6 @@ jlmol is an Electron-based desktop application for molecular visualization built
   npm run start-safe-debug
   ```
 
-- Debug GPU capabilities:
-  ```bash
-  npm run debug-gpu
-  ```
 
 ### Building
 - Build for Linux:
@@ -99,7 +90,7 @@ jlmol is an Electron-based desktop application for molecular visualization built
 
 ### Basic Molecular Viewer Testing
 1. Start the application: `npm start`
-2. Load a sample molecule from jsmol/data/ directory (drag and drop or file menu)
+2. Load a sample molecule (Caffeine/Buckyball buttons) or open a structure file
 3. Test rotation: Click and drag to rotate the molecule
 4. Test display modes: Switch between ball&stick, wireframe, spacefill
 5. Test spin animation: Enable/disable spin controls
@@ -138,16 +129,13 @@ jlmol is an Electron-based desktop application for molecular visualization built
 - `.github/workflows/release.yml` - Automated build and release pipeline
 
 ### Important Directories
-- `jsmol/` - JSmol molecular viewer library and sample data files
-- `jsmol/data/` - Sample molecular structure files (PDB, XYZ, CIF, etc.)
+- `jsmol/` - JSmol molecular viewer library (`jsmol/data/` holds only the two sample molecules)
 - `build/` - Application icons and build resources
 - `scripts/` - Utility scripts including `runremote` for remote Julia execution
-- `legacy/` - Legacy test files and older JSmol implementations
 - `dist/` - Build output directory (created after running build commands)
 
 ### Configuration Files
 - `.gitignore` - Git ignore patterns
-- `VERSION-MANAGEMENT.md` - Documentation for version management system
 - `Troubleshooting.md` - User troubleshooting guide
 - `CHANGELOG.md` - Project change history
 
@@ -156,7 +144,6 @@ jlmol is an Electron-based desktop application for molecular visualization built
 ### Version Management
 - Version is defined ONLY in package.json
 - All other files use dynamic version loading
-- Run `npm run check-version` to verify consistency
 - Never hardcode versions in HTML, JS, or other files
 
 ### Julia/ElemCo.jl Integration
@@ -168,8 +155,7 @@ jlmol is an Electron-based desktop application for molecular visualization built
 ### Troubleshooting Graphics Issues
 - Windows 11 users may need hardware acceleration disabled
 - Use `npm run start-safe` for GPU-related problems
-- Use `npm run debug-gpu` for comprehensive GPU analysis
-- Check WINDOWS11-FIX-SUMMARY.md for platform-specific solutions
+- See Troubleshooting.md for platform-specific solutions
 
 ### Database Integration
 - PubChem integration requires internet connection

CHANGELOG.md

@@ -17,6 +17,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Image export and XYZ export in the desktop app now open a save dialog instead of dropping the file silently into the download folder. The dialog defaults to the launch directory when started from a terminal and to the download folder otherwise; the status line shows where the file was saved, or that the export was cancelled.
 - "Choose File" in the desktop app is replaced by an "Open File…" button with a native open dialog that starts in the launch directory when there is one (the browser file picker cannot be pointed at a directory, and its "No file chosen" label would stay stale). The loaded file's name is shown next to the button. Without a launch directory the OS chooses the folder as before. The browser build keeps the file input.
 
+### Removed
+
+- Repository clutter that was never part of the app: the `legacy/` JSmol demo pages (292 files), JSmol's sample data in `jsmol/data/` except the two sample molecules the buttons load (39 MB, previously shipped in every installer), the unused `jsmol/js/JSmolJME.js`, the icon drafts `build/icon_benzene*.svg` and `build/icon_detailed.svg`, and the June 2025 leftovers `WINDOWS11-FIX-SUMMARY.md`, `VERSION-MANAGEMENT.md`, `build-version.js` (`npm run check-version`) and `debug-gpu.js` (`npm run debug-gpu`). `Troubleshooting.md` covers what those documents said.
+
 ## [1.5.5] - 2026-09-07
 
 ### Fixed

Troubleshooting.md

@@ -23,25 +23,15 @@ jlmol.exe --disable-hardware-acceleration
 - Update your graphics card drivers to the latest version
 - Consider switching between integrated and discrete graphics
 
-### Option 3: Run GPU Debug Tool
-
-For comprehensive system analysis:
-
-```bash
-npm run debug-gpu
-```
-
-This will generate a detailed report of your GPU capabilities and test different configurations.
-
-### Option 4: Run in Safe Mode
+### Option 3: Run in Safe Mode
 
 For debugging issues:
 
 ```bash
 npm run start-safe-debug
 ```
 
-### Option 5: Check System Resources
+### Option 4: Check System Resources
 
 - Close other graphics-intensive applications
 - Monitor memory usage (Task Manager)
@@ -115,12 +105,6 @@ jlmol supports loading structures directly from the PubChem database:
 
 ## Additional Support
 
-For more detailed troubleshooting information and platform-specific fixes, see:
-
-- [WINDOWS11-FIX-SUMMARY.md](WINDOWS11-FIX-SUMMARY.md) - Windows 11 specific solutions
-- [DISPLAY_MODE_FIX_COMPLETE.md](DISPLAY_MODE_FIX_COMPLETE.md) - Display mode button fixes
-- [ELEMCO_FIX_COMPLETE.md](ELEMCO_FIX_COMPLETE.md) - ElemCo.jl integration fixes
-
 If you encounter issues not covered here, please check the GitHub issues or create a new issue with details about your system and the specific problem.
 
 ## xtb (g-xTB) Calculations