Generalize workflow authentication validation

[adampoit]

Summary

• validate authentication token flow from custom action outputs, shell-step outputs, and Actions secrets while retaining strict checks for the generated GitHub App action
• prompt users to choose an authentication approach and preserve established credential inputs and names
• remove the limited verify-auth command and its workflow correlation inputs in favor of validating the first workflow-driven published sync
• update migration, setup, configuration, generated workflow, and bundled skill guidance

Testing

• npm test (85 tests)
• npm run format:check
• LSP diagnostics

Closes #59

[not-adam]

Mira PR Walkthrough

This PR generalizes Patchlane's workflow authentication validation from a rigid actions/create-github-app-token-only model to support custom action outputs, shell-step outputs, and Actions secrets. The doctor command now inspects the data flow of authentication tokens rather than enforcing a single hardcoded source, while retaining strict checks for the generated GitHub App path. The limited verify-auth command is removed in favor of validating authentication during the first workflow-driven published sync. Documentation, skill guidance, and bundled assets are updated accordingly.

graph LR
    doctor["src/doctor.ts"]
    cli["src/cli.ts"]
    tests["tests/doctor.test.ts"]
    skill["skills/.../SKILL.md"]
    docs["docs/configuration.md"]
    doctor --> tests
    cli --> doctor

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Confidence: 5/5   ◉◉◉◉◉   Safe to merge

• Well-structured refactor with comprehensive test coverage (78 lines added to tests), no behavioral regressions for the existing generated GitHub App path, and documentation updated across all relevant surfaces.

Blast Radius — 2 dependent repositories, 3 total references

adampoit/mira — 1 reference
adampoit/wezterm — 2 references

10 files reviewed

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Comment @not-adam help to get the list of available commands and usage tips.