unpack-trees: do not check for conflict entries too early

unpack-trees: do not check for conflict entries too early

The idea of sparse checkout is conflict entries should always stay
in worktree, regardless $GIT_DIR/info/sparse-checkout. Therefore,
ce_stage(ce) usually means no CE_SKIP_WORKTREE. This is true when all
entries have been merged into the index, and identical staged entries
collapsed.

However, will_have_skip_worktree() since f1f523e (unpack-trees():
ignore worktree check outside checkout area) is also used earlier in
verify_* functions, where entries have not been merged to index yet
and ce_stage() is not zero. Checking ce_stage() then may provoke
unnecessary verification on entries outside checkout area and error
out.

This fixes part of test case "read-tree adds to worktree, dirty case".
The error

error: Untracked working tree file 'sub/added' would be overwritten by merge.

is now gone and (unfortunately) replaced by another error, which will
be addressed in the next patch.

Signed-off-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com>
Reviewed-by: Jonathan Nieder <jrnieder@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>