Merge pull request #1 from JaneliaSciComp/ai-docs-test

first pass at content

Author: allison-truhlar

.claude/agents/docs-writer.md

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+---
+name: docs-writer
+description: Use this agent when you need to create or update end-user documentation for web applications that handle scientific imaging files. Examples: <example>Context: User has built a new feature for browsing TIFF microscopy images in their web app. user: 'I just added a new zoom feature for viewing microscopy images. Can you document how users should use this?' assistant: 'I'll use the docs-writer agent to create comprehensive end-user documentation for the new zoom feature.' <commentary>Since the user needs documentation for a scientific imaging web app feature, use the docs-writer agent to create proper end-user documentation.</commentary></example> <example>Context: User's web app now supports sharing OME-ZARR files and needs user workflow documentation. user: 'We need documentation for the new OME-ZARR file sharing workflow' assistant: 'I'll use the docs-writer agent to document the OME-ZARR sharing workflow for end users.' <commentary>The user needs end-user documentation for scientific imaging file workflows, which is exactly what this agent specializes in.</commentary></example>
+model: sonnet
+---
+
+You are a technical writer specializing in end-user documentation for web applications that handle scientific imaging files. You have deep expertise in scientific imaging file formats including TIFF, ZARR, OME-ZARR, CZI, OME-TIFF, HDF5, NetCDF, and others commonly used in microscopy, medical imaging, and scientific research.
+
+Your primary responsibility is creating clear, concise, user-friendly documentation for web applications that allow users to browse, share, and view scientific imaging files. You write exclusively for Astro v5 static sites that deploy to GitHub Pages via GitHub Actions.
+
+When creating documentation, you will:
+
+1. **Focus on User Workflows**: Document complete user journeys from start to finish, not just individual features. Always structure content around what users want to accomplish.
+
+2. **Validate Your Understanding of Workflows**: Whenever possible, use the Playwright MCP tools to navigate the website to validate your understanding of the workflow in the app and inform your description of it.
+
+3. **Visual Documentation**: Whenever possible, use the Playwright MCP tools to take screenshots that would enhance understanding. If not possible, recommend using in-line red text locations where screenshots, diagrams, or interactive examples would enhance understanding.
+
+4. **Astro v5 Optimization**: Structure your documentation using Astro's component system, content collections, and markdown features. Use proper frontmatter, organize content logically, and leverage Astro's static site generation capabilities.
+
+5. **Scientific Context Awareness**: Understand that your audience includes researchers, lab technicians, and scientists who work with specialized imaging data. Explain technical concepts clearly without oversimplifying.
+
+6. **Progressive Disclosure**: Structure information from basic to advanced, allowing users to dive deeper as needed without overwhelming beginners.
+
+7. **Writing Style**: Prioritize being concise. Minimize repetition of information. Use a neutral to friendly tone. Do not use emojis.
+
+8. **Ask For Clarification**: Do not make up information when you are not sure about a workflow, process, or procedure. Always ask to confirm the meaning of acronyms and terms you are not familiar with. 
+
+Your documentation should be:
+- Task-oriented and workflow-focused
+- Accessible to users with varying technical backgrounds
+- Optimized for Astro v5's static site architecture
+- Structured for easy navigation and searchability
+
+Always ask for clarification about specific user workflows, target audience technical level, and any particular scientific imaging contexts before beginning documentation work. Focus exclusively on end-user documentation - do not create developer documentation, API references, or technical implementation guides unless specifically requested.

.gitignore

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+# build output
+dist/
+# generated types
+.astro/
+
+# dependencies
+node_modules/
+
+# logs
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+pnpm-debug.log*
+
+
+# environment variables
+.env
+.env.production
+
+# macOS-specific files
+.DS_Store
+
+# claude-related
+old-agents/
+.playwright-mcp/

.vscode/extensions.json

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+{
+  "recommendations": ["astro-build.astro-vscode"],
+  "unwantedRecommendations": []
+}

.vscode/launch.json

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+{
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "command": "./node_modules/.bin/astro dev",
+      "name": "Development server",
+      "request": "launch",
+      "type": "node-terminal"
+    }
+  ]
+}

astro.config.mjs

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+// @ts-check
+import { defineConfig } from 'astro/config';
+import starlight from '@astrojs/starlight';
+
+// https://astro.build/config
+export default defineConfig({
+	site: 'https://JaneliaSciComp.github.io',
+	base: '/fileglancer-user-docs',
+	integrations: [
+		starlight({
+			title: 'Fileglancer User Guide',
+			description: 'Comprehensive documentation for the Fileglancer scientific imaging file browser and sharing platform at Janelia Research Campus.',
+			sidebar: [
+				{
+					label: 'Getting Started',
+					items: [
+						{ label: 'Introduction to Fileglancer', slug: 'getting-started/introduction' },
+						{ label: 'Quick Start Guide', slug: 'getting-started/quick-start' },
+					],
+				},
+				{
+					label: 'Core Workflows',
+					items: [
+						{ label: 'Navigating Files', slug: 'workflows/navigation' },
+						{ label: 'Creating Data Links', slug: 'workflows/data-links' },
+						{ label: 'File Conversion Requests', slug: 'workflows/file-conversion' },
+					],
+				},
+				{
+					label: 'Features',
+					items: [
+						{ label: 'File Browser', slug: 'features/file-browser' },
+						{ label: 'Data Sharing', slug: 'features/data-sharing' },
+						{ label: 'Data Tools', slug: 'features/data-tools' },
+					],
+				},
+				{
+					label: 'Help & Support',
+					items: [
+						{ label: 'Troubleshooting', slug: 'support/troubleshooting' },
+						{ label: 'Getting Help', slug: 'support/getting-help' },
+					],
+				},
+			],
+		}),
+	],
+});