Reorganize repository structure and clean up documentation

Clean up and organize the flask-shopdb repository for better
maintainability and discoverability:

## Changes

- Update .gitignore for build artifacts (publish/, data/, 122M total)
- Reorganize .claude/ into 6 subdirectories with README navigation
- Consolidate overlapping MCP setup guides into MCP-QUICK-START.md
- Move deployment docs from root to docs/deployment/
- Archive dated status reports to .claude/archived/
- Delete temporary files (logs, backups, empty reports, ~50K)

## New Structure

.claude/ organized into:
- setup/ - MCP, VM, Hyper-V, GitHub setup guides + scripts (17 files)
- plans/ - Feature plans and protocols (5 files)
- maintenance/ - Deployment checklists and reports (4 files)
- archived/ - Historical documentation (9 files)
- skills/ - Claude Code automation (5 files)
- workflows/ - Security audit workflow (1 file)

docs/deployment/ created with 6 deployment guides:
- LOCAL-DEV-SETUP.md, DOCKER-SETUP.md, DOCKER-PREBUILT-APPROACH.md
- PRODUCTION-READINESS.md, DEPLOY-TO-VM.md, README.md

Root directory cleaned to essential docs only:
- CLAUDE.md, README.md, CONTRIBUTING.md, CHANGELOG.md

Benefits:
- Clear navigation via README.md in each subdirectory
- No duplicate/overlapping documentation
- Large artifacts properly gitignored (won't bloat repository)
- Historical context preserved in archived/

See .claude/CLEANUP-SUMMARY.md for complete details.

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

.claude/setup/GITHUB-MCP-SETUP.md

@@ -0,0 +1,71 @@
+# GitHub MCP Setup Guide
+
+The GitHub MCP server failed to connect with error:
+```
+Authorization header is badly formatted
+```
+
+## Fixing the GitHub MCP Connection
+
+1. **Check MCP configuration** (likely in `.claude/mcp.json` or Claude app settings):
+   ```json
+   {
+     "mcpServers": {
+       "github": {
+         "command": "...",
+         "args": [...],
+         "env": {
+           "GITHUB_TOKEN": "your-token-here"
+         }
+       }
+     }
+   }
+   ```
+
+2. **Verify GitHub token**:
+   - Token should be a GitHub Personal Access Token (PAT)
+   - Required scopes: `repo`, `read:org`
+   - Generate at: https://github.com/settings/tokens
+
+3. **Token format**:
+   - Classic PAT: `ghp_...` (starts with ghp_)
+   - Fine-grained PAT: `github_pat_...`
+   - No extra quotes or whitespace
+
+4. **Common issues**:
+   - Token expired (regenerate on GitHub)
+   - Wrong token format (not base64 encoded, just raw token)
+   - Authorization header format (should be `Bearer <token>` or `token <token>`)
+
+5. **Test token manually**:
+   ```bash
+   curl -H "Authorization: token YOUR_TOKEN" https://api.github.com/user
+   ```
+
+## What GitHub MCP Would Enable
+
+Once connected, I could:
+- Create PRs directly from conversation
+- Check CI/CD status
+- Link commits to issues
+- Review PR comments
+- Update issue status
+
+## Alternative: Manual Git + GitHub CLI
+
+If MCP stays broken, you can use `gh` CLI:
+```bash
+# Install GitHub CLI if not present
+winget install --id GitHub.cli
+
+# Authenticate
+gh auth login
+
+# I can then use gh commands via Bash tool
+gh pr create --title "..." --body "..."
+gh pr status
+```
+
+## To Diagnose
+
+Check Claude Code settings or MCP config file for the github server configuration and verify the token is valid.