unpack-trees: add progress to clear_ce_flags()

unpack-trees: add progress to clear_ce_flags()

When a large repository has many sparse-checkout patterns, the
process for updating the skip-worktree bits can take long enough
that a user gets confused why nothing is happening. Update the
clear_ce_flags() method to write progress.

Signed-off-by: Derrick Stolee <redacted>
Signed-off-by: Junio C Hamano <redacted>