Remove dead code that was inadvertently orphaned when PR #918 refactored
the sync flow. The function was never called since v0.47.0.
The function caused GH#1100 by running `git checkout HEAD -- .beads/`
which restored the entire .beads/ directory, overwriting uncommitted
config.yaml changes.
Add regression test (TestConfigPreservedDuringSync) to prevent similar
restoration logic from being reintroduced.
Fixes#1100
5d93aaf722