Add script-run repo update warnings with opt-in auto-pull and local-change handling

[Copilot]

🧾 PR Checklist

Script execution now detects when the underlying git-backed repo is behind upstream and surfaces a non-blocking warning by default. It also adds an opt-in --auto-pull-repo flow that handles local modifications safely instead of prompting on every run.

• Default update signal (no forced prompt)

  • Detects upstream divergence for the selected script repo on top-level runs.
  • Warns with commit lag and changed file list (capped for readability).

• Script-specific relevance

  • Flags when the currently selected script path is included in upstream changes.

• Opt-in auto update

  • Adds auto_pull_repo / MLC_AUTO_PULL_REPO handling.
  • With local changes:
    • interactive mode: choose keep/discard/cancel
    • quiet mode: skip auto-pull safely
  • Pull path uses fast-forward-only semantics.

• Resilience

  • Adds bounded git command timeouts.
  • Replaces hardcoded operational values with named constants.

# simplified flow added in script run path
status = _get_repo_update_status(repo_path, script_relative_path)
if status["update_available"]:
    warn_changed_files(status)
    if auto_pull_repo:
        _auto_pull_repo_updates(repo_path, quiet, logger, recursion_spaces)

• Target branch is dev

📌 Note: PRs must be raised against dev. Do not commit directly to main.

📁 File Hygiene & Output Handling

• No unintended files (e.g., logs, cache, temp files, pycache, output folders) are committed

📝 Comments & Communication

• Proper inline comments are added to explain important or non-obvious changes
• PR title and description clearly state what the PR does and why
• Related issues (if any) are properly referenced (Fixes #, Related to #, etc.)

🛡️ Safety & Security

• No secrets or credentials are committed
• Paths, shell commands, and environment handling are safe and portable