checkout-index: add --ignore-skip-worktree-bits option

Update `checkout-index` to no longer refresh files that have the
`skip-worktree` bit set, exiting with an error if `skip-worktree` filenames
are directly provided to `checkout-index`. The newly-added
`--ignore-skip-worktree-bits` option provides a mechanism to replicate the
old behavior, checking out *all* files specified (even those with
`skip-worktree` enabled).

The ability to toggle whether files should be checked-out based on
`skip-worktree` already exists in `git checkout` and `git restore` (both of
which have an `--ignore-skip-worktree-bits` option). The change to, by
default, ignore `skip-worktree` files is especially helpful for
sparse-checkout; it prevents inadvertent creation of files outside the
sparse definition on disk and eliminates the need to expand a sparse index
when using the `--all` option.

Internal usage of `checkout-index` in `git stash` and `git filter-branch` do
not make explicit use of files with `skip-worktree` enabled, so
`--ignore-skip-worktree-bits` is not added to them.

Helped-by: Elijah Newren <newren@gmail.com>
Signed-off-by: Victoria Dye <vdye@github.com>
Reviewed-by: Elijah Newren <newren@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>
diff --git a/Documentation/git-checkout-index.txt b/Documentation/git-checkout-index.txt
index 4d33e7b..01dbd5c 100644
--- a/Documentation/git-checkout-index.txt
+++ b/Documentation/git-checkout-index.txt
@@ -12,6 +12,7 @@
 'git checkout-index' [-u] [-q] [-a] [-f] [-n] [--prefix=<string>]
 		   [--stage=<number>|all]
 		   [--temp]
+		   [--ignore-skip-worktree-bits]
 		   [-z] [--stdin]
 		   [--] [<file>...]
 
@@ -37,8 +38,9 @@
 
 -a::
 --all::
-	checks out all files in the index.  Cannot be used
-	together with explicit filenames.
+	checks out all files in the index except for those with the
+	skip-worktree bit set (see `--ignore-skip-worktree-bits`).
+	Cannot be used together with explicit filenames.
 
 -n::
 --no-create::
@@ -59,6 +61,10 @@
 	write the content to temporary files.  The temporary name
 	associations will be written to stdout.
 
+--ignore-skip-worktree-bits::
+	Check out all files, including those with the skip-worktree bit
+	set.
+
 --stdin::
 	Instead of taking list of paths from the command line,
 	read list of paths from the standard input.  Paths are