sync should not auto-stage modified files

[krisrowe]

Problem

dot sync currently stages and commits all modified tracked files automatically. This means changes get pushed to GitHub without any review step — if a tracked file was modified unintentionally or contains something unexpected, it gets committed and pushed silently.

Desired behavior

dot sync should only commit and push files that have been explicitly staged (e.g., via a dot add command or equivalent). Modified-but-unstaged tracked files should not be auto-committed.

Open question

What should dot sync do when there are unstaged changes to tracked files?

Options to consider:

• Warn and refuse to sync until changes are explicitly staged or discarded
• Sync only what's staged, silently ignore unstaged changes
• Prompt or report what would be left behind

The key principle: no changes should leave the machine without an explicit review/add step.