Integrate GitHub App token generation directly into backup tool with automatic refresh

[Copilot]

This PR completely redesigns the GitHub App authentication approach to eliminate complexity and provide a much simpler user experience. Instead of requiring external scripts and manual token management, the backup tool now handles GitHub App authentication internally.

What Changed

Before (Complex):

• Users had to create external Python scripts to generate tokens
• Required complex cron job setups with token refresh logic
• Manual handling of 1-hour token expiry during long backups
• Multiple files and dependencies to manage

After (Simple):

# Direct GitHub App authentication - no external scripts needed
github-backup myorg \
    --app-id 123456 \
    --installation-id 789012 \
    --private-key /path/to/app-private-key.pem \
    --organization \
    --repositories

Key Features

• Internal Token Management: Tool automatically generates and refreshes GitHub App installation tokens as needed
• Automatic Expiry Handling: Seamlessly handles the 1-hour token expiry during long-running organization backups
• Simple CLI Arguments: Three new arguments (--app-id, --installation-id, --private-key) replace complex external scripts
• Docker-Friendly: Works perfectly with mounted private key files in containerized environments
• Smart Validation: Clear error messages guide users when credentials are missing or conflicting
• Backwards Compatible: Existing --token + --as-app approach continues to work

Benefits

• Eliminates Setup Complexity: No more external token generation scripts or cron job token management
• Production Ready: Handles token refresh automatically during multi-hour backups without interruption
• Enterprise Friendly: Simple to deploy in containerized environments with proper credential management
• Developer Experience: Clear error messages and validation help users get set up quickly

This addresses the feedback that the previous approach was "way too complicated" by moving all the complexity into the tool itself, providing a clean and simple interface for users.

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[schlomo]

@copilot When installing the new app I had to create a client secret, how do I go from client secret to token? The docs should reflect a setup where the backup runs nightly e.g. via cron job

[Copilot]

@copilot When installing the new app I had to create a client secret, how do I go from client secret to token? The docs should reflect a setup where the backup runs nightly e.g. via cron job

I've updated the documentation to properly address the client secret to token conversion process. The documentation now includes:

1. Complete token generation script: A full Python script that uses your GitHub App's private key (not client secret) to generate installation access tokens
2. Cron job setup: Step-by-step instructions for automated nightly backups including environment variables and a complete backup script
3. Credential clarification: Clear explanation of what each credential is used for (App ID, Installation ID, private key)

The key insight is that for automated token generation, you use the private key (not the client secret) along with the App ID and Installation ID. The client secret is primarily used for OAuth flows, not for this programmatic token generation approach.

See commit 08dbe62 for the complete automated backup setup documentation.

[schlomo]

@copilot explain why we use a classic token and not a fine grained token. Explain what happens if the backup takes longer than 1h. Is it a problem if the token expires before the backup is done? How can we remediate that, e.g. regenarating the token if needed till the backup is done?

[Copilot]

@copilot explain why we use a classic token and not a fine grained token. Explain what happens if the backup takes longer than 1h. Is it a problem if the token expires before the backup is done? How c...

I've added comprehensive documentation explaining these important technical aspects:

Classic vs Fine-Grained Tokens: Classic tokens are required with --as-app because GitHub App installation tokens follow the classic format (ghs_ prefix) and use app-specific API headers. Fine-grained tokens are designed for user-scoped access, not app authentication.

Token Expiry Handling: The 1-hour expiry is indeed a problem for long backups. When tokens expire mid-backup, you get 401 Unauthorized errors and the backup fails with incomplete data.

Solutions Provided: Three production-ready strategies:

1. Pre-emptive refresh: Monitor backup duration and refresh tokens every 50 minutes
2. Segmented backup: Break large backups into chunks (repos, issues, metadata) that complete within 1 hour
3. Error-resilient: Use incremental backups with retry logic and fresh tokens

The segmented approach is recommended for nightly cron jobs as it's most predictable and recovery-friendly.

See commit 95358a4 for the complete documentation with working scripts.

[schlomo]

@copilot I think that this is way too complicated. Why not simply add the token generation into the backup tool so that we can provide the backup tool with the private key instead of a token. The backup tool should then use that to generate tokens as needed. This will also simplify using this mode in Docker. double check the resulting code for correctness and clarity and simplicity for the user

[Copilot]

@copilot I think that this is way too complicated. Why not simply add the token generation into the backup tool so that we can provide the backup tool with the private key instead of a token. The back...

You're absolutely right! I've completely redesigned the approach to be much simpler and more user-friendly.

What's Changed:

✅ Direct GitHub App Integration: No more external scripts - the backup tool now handles token generation internally
✅ Simple CLI Arguments: Just use --app-id, --installation-id, and --private-key directly
✅ Automatic Token Management: Tool handles token expiry and refresh automatically during long backups
✅ Docker-Friendly: Works perfectly with mounted private key files

New Usage (Much Simpler):

github-backup YOUR_ORG \
    --app-id 123456 \
    --installation-id 789012 \
    --private-key /path/to/your-app.pem \
    --organization \
    --repositories

Key Benefits:

• No manual token generation scripts needed
• No complex cron job setups
• Automatic token refresh during multi-hour backups
• Environment variables work great for security
• Simple to containerize

The documentation is now focused on the essential steps: create GitHub App → get credentials → run backup. All the complex token management is handled internally.

See commit 3296835 for the complete implementation.