docs: improve QuiltSync documentation structure

docs/SUMMARY.md

@@ -81,3 +81,4 @@
 * [Benchling Packager](examples/benchling.md)
 * [Event-Driven Packaging](advanced-features/event-driven-packaging.md)
 * [Nextflow Plugin](examples/nextflow.md)
+* [QuiltSync Desktop Application](examples/quiltsync.md)

docs/examples/quiltsync.md

@@ -1,84 +1,79 @@
 # QuiltSync
 
-**Desktop client for seamless access to versioned, AI-ready datasets.**
+QuiltSync is a desktop application for syncing versioned Quilt data packages to
+your local machine. It provides local access to Quilt packages stored in S3,
+with support for Windows 10+, macOS 10.14+ (Intel & Apple Silicon), and Linux.
 
-Visit [quilt.bio/quiltsync](https://quilt.bio/quiltsync/) to download the
-latest version.
+Download: [quilt.bio/quiltsync](https://quilt.bio/quiltsync/)
 
-QuiltSync is a desktop application from Quilt Data that enables scientists,
-researchers, and engineers to access, manage, and version large datasets
-locally. Install once and seamlessly sync Quilt data packages (versioned,
-AI/ML-ready datasets) to your computer across Windows, macOS (Intel & Apple
-Silicon), and Linux.
+## Features
+
+- Browse and sync packages via graphical interface
+- Selective file sync to manage disk space
+- Version control for data packages
+- Browser-based authentication
 
 ## Getting Started
 
-When viewing packages in the Quilt web catalog, you can open them directly in
-QuiltSync:
+### Installation
 
-1. Navigate to a package in your Quilt catalog
-2. Click the "Get Package" button and select "QuiltSync"
-3. QuiltSync will open automatically (if installed) and begin syncing the
-   package
+Download and install QuiltSync from
+[quilt.bio/quiltsync](https://quilt.bio/quiltsync/).
 
-### Integration with Benchling
+### Opening Packages and Files
 
-QuiltSync integrates with the [Benchling Webhook](./benchling.md) to provide
-seamless access to notebook-linked packages:
+From the Quilt web catalog:
+
+1. Navigate to a package or file
+2. Click "Get Package" or "Get File"
+3. Select "Open in QuiltSync"
 
-- In Benchling's App Canvas, click the "sync" button next to any package
-- The package or file will open directly in QuiltSync
-- Changes and updates are reflected across both platforms
+![Open in QuiltSync](../imgs/quiltsync-open.png)
 
-## Overview
+### Authentication
 
-QuiltSync brings the power of Quilt data packages to your desktop, providing
-a local sync solution for cloud-stored data. While datasets may live in
-remote storage (S3), QuiltSync gives you local access so you can work offline
-or interact with datasets as if they're on your machine.
+On first use, QuiltSync prompts for authentication via your web browser:
 
-## Key Features
+1. QuiltSync opens your browser to the Quilt Catalog login page
+2. Sign in to your catalog
+3. Access token is automatically provided to QuiltSync
 
-### Versioned Data Packages
+The token is tied to your catalog session. No AWS credentials required.
 
-QuiltSync doesn't just pull files—Quilt packages include version control for
-data, tracking changes and enabling reproducible workflows. Each package has
-a complete version history, allowing you to:
+### Selective Installation
 
-- Track data changes over time
-- Roll back to previous versions
-- Ensure reproducible analysis and ML workflows
-- Collaborate with confidence that everyone uses the same data version
+Select which files to sync:
 
-### Desktop/Local Access
+- Use checkboxes to select files or folders
+- Click "SELECT ALL" for entire package
+- Review file sizes before installing
+- Click "INSTALL" to sync selected files
 
-Even though data lives in cloud storage, QuiltSync provides local sync
-capabilities:
+### Settings and Troubleshooting
 
-- Work offline with synced datasets
-- Interact with S3 data as if it's on your local machine
-- Reduce latency for data-intensive operations
-- Control which packages and versions are synced locally
+Access settings via the gear icon in the lower right:
 
-### AI-Ready Format
+![QuiltSync Settings](../imgs/quiltsync-settings.png)
 
-The platform targets researchers, machine learning engineers, and data science
-teams who need clean, versioned datasets prepared for AI/ML pipelines:
+- **Version**: Current version and release notes
+- **Lineage and cache files**: Opens `.quilt/` directory with package metadata
+- **Logs directory**: Application logs for debugging
+- **Reset state**: "RELOAD PAGE" refreshes UI, "RE-LOGIN" clears authentication
+
+### Integration with Benchling
+
+QuiltSync integrates with the [Benchling Webhook](./benchling.md) to provide
+seamless access to Quilt packages from Benchling notebooks.
 
-- Datasets formatted for machine learning workflows
-- Metadata and schema validation
-- Integration with data science tools and notebooks
-- Support for large-scale data operations
+![Benchling App Canvas](../imgs/benchling-canvas.png)
 
-## System Requirements
+When viewing a package in the Benchling App Canvas:
 
-QuiltSync runs on all major operating systems:
+1. Click the "sync" button next to any package or file
+2. QuiltSync automatically opens with the selected package
+3. Select files to sync locally
+4. Work offline with your data
 
-- **Operating Systems**: Windows 10+, macOS 10.14+, Linux (modern
-  distributions)
-- **Disk Space**: Varies based on package sizes you plan to sync (consider
-  storage for large datasets)
-- **Network**: Internet connection required for syncing with S3 (bandwidth
-  considerations for large datasets)
-- **AWS Access**: Valid AWS credentials configured for accessing your Quilt
-  buckets
+This integration allows scientists to move from notebook entries to local
+datasets without leaving their Benchling workflow. For more details, see
+[Benchling App Canvas](./benchling.md#benchling-app-canvas).