feat(auth): implement GitHub token setup for private repos and higher rate limits

[calchiwo]

This PR introduces a config GitHub authentication flow using explainthisrepo init.

Before:

• GitHub access relied on environment variables only
• CLI exposed experimental --token flags
• Private repos failed silently or with unclear errors
• Rate limit errors were not actionable

After:

• GitHub token can be configured once via init
• Token is stored in config and automatically resolved
• All GitHub calls use a unified auth pipeline
• CLI no longer exposes --token flags
• Errors now guide users to fix auth via init or env

Changes

• init.py

  • prompt for optional GitHub token during setup
  • persist token under [github] config section

• github.py

  • resolve token from:
    1. CLI override (future-safe)
    2. config file
    3. environment variables
  • attach token to all requests via shared session
  • improve rate limit and private repo error messages

• repo_reader.py

  • propagate token through fetch_tree and fetch_file
  • ensure all repository reads use authenticated requests

• cli.py

  • remove --token flags
  • add GitHub auth guidance to help output
  • surface token status in --doctor

Impact

• enables access to private repositories
• increases GitHub API rate limits when configured
• improves UX by making auth setup explicit and centralized
• removes inconsistent CLI-based auth paths

Notes

• auth is optional; public repos continue to work without configuration
• environment variables (GITHUB_TOKEN, GH_TOKEN) are still supported
• this establishes a single source of truth for GitHub authentication

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Project	Deployment	Actions	Updated (UTC)
explainthisrepo	Ready	Preview, Comment	Mar 24, 2026 4:04am

[calchiwo]

See #157