refresh_index(): add flag to ignore SKIP_WORKTREE entries

refresh_index(): add flag to ignore SKIP_WORKTREE entries

refresh_index() doesn't update SKIP_WORKTREE entries, but it still
matches them against the given pathspecs, marks the matches on the
seen[] array, check if unmerged, etc. In the following patch, one caller
will need refresh_index() to ignore SKIP_WORKTREE entries entirely, so
add a flag that implements this behavior.

While we are here, also realign the REFRESH_* flags and convert the hex
values to the more natural bit shift format, which makes it easier to
spot holes.

Signed-off-by: Matheus Tavares <matheus.bernardino@usp.br>
Signed-off-by: Junio C Hamano <gitster@pobox.com>