v0.1.1: Refinements — interactive init, config-backed run, Git LFS hook tolerance, graceful shutdown

[rpothin]

Summary

This PR implements the v0.1.0 refinement plan improvements focused on first-run UX, clearer CLI semantics, safer config usage, and more resilient git/codespaces behavior. It also bumps the package version to 0.1.1.

Addresses findings from plans/v0-1-0_REFINEMENT_PLAN.md

• Finding 1 (init UX): ghcralph init is now interactive by default in TTYs (review defaults → edit values → confirm write), with option lists for plan source/model/auto-commit.
• Finding 2 (file/plan confusion): --plan removed; --file now supports both single-task files and Markdown plan files (auto-detected).
• Finding 3 (GitHub plan source defaults): configuration schema extended with GitHub plan settings (githubRepo + optional filters). init prompts for them when planSource=github.
• Finding 4 (avoid overriding config via flags): run now treats config as the source of truth for maxIterations/maxTokens/defaultModel/autoCommit/branchPrefix; CLI flags removed where appropriate.
• Finding 5 (dry-run model mismatch): run --dry-run now loads config and displays/uses defaultModel consistently.
• Finding 6 (first run error + shutdown hang):
  • GitBranchManager now tolerates failing git hooks (e.g. missing git-lfs) when the branch was actually created/checked out, and prints a warning instead of throwing.
  • Copilot session cleanup improved (uses sendAndWait()), plus run now cleans up SIGINT/SIGTERM handlers and destroys the agent on exit.

Docs / Devcontainer

• Updated docs (including cookbook troubleshooting) to explain Git LFS hook errors and mitigation options.
• Devcontainer adjusted to avoid requiring Git LFS by default.
• Minor CLI help example fix for GitHub issues workflow.

Release

• Bumped package.json and package-lock.json to 0.1.1.

Validation

• npm run lint
• npm run typecheck
• npm test
• npm run build