Changed to index file + use real ObjectStore

[Saanvi521]

Summary

• Index is now a real file on disk which replaces Week 1's in-memory self._entries
• Modified all functions accordingly
• minigit status now prints staged / not staged / untracked sections in order, skipping empty sections, or printing clean if nothing to report
• Switched tests to the real ObjectStore (dropped FakeObjectStore)

Validation

• scripts/quality-check.sh
• Manual testing, if applicable:

Checklist

• The change is focused and easy to review.
• Tests were added or updated for behavior changes.
• Documentation was updated for user-facing or setup changes.
• No secrets, generated artifacts, or local-only files are included.

Notes for Reviewers