feat(init): prompt for git policy

[rochecompaan]

Summary

• Replace the broad init local-only warning with an interactive git policy choice.
• Support add-to-git, .gitignore, and .git/info/exclude handling, with non-interactive/--yes defaulting to local exclude.
• Protect Patchmill runtime/auth/session directories when committing config and skills, and harden edge cases for custom/no skill roots and local exclude failures.

Test Plan

• npm test
• npm run lint:ts
• npm run format:check
• npx markdownlint-cli2 docs/configuration.md docs/specs/2026-06-13-init-git-policy-prompt-design.md docs/plans/2026-06-13-init-git-policy-prompt.md