checkout: gracefully handle files deleted from the index

Right now, when someone deletes a pointer from the index with `git rm`
and then runs `git lfs checkout`, the operation fails with a message of
"Could not update the index" because our invocation of `git
update-index` is missing the `--add` flag.

Obviously, the user does not expect an error in this case, and `git
checkout` simply ignores files staged for deletation, so let's do the
same thing.  If a file on disk is deleted, check the index with `git
diff-index` to see if it's deleted from `HEAD`.  If so, ignore the file,
just like Git does. Note that we use `git diff-index` specifically
because it doesn't refresh the index and is therefore much cheaper than
alternatives, such as `git status`, which might do that.

commands/pull.go

@@ -4,6 +4,7 @@ import (
 	"bytes"
 	"io"
 	"os"
+	"strings"
 	"sync"
 
 	"github.com/git-lfs/git-lfs/v3/config"
@@ -69,7 +70,19 @@ func (c *singleCheckout) Run(p *lfs.WrappedPointer) {
 
 	// Check the content - either missing or still this pointer (not exist is ok)
 	filepointer, err := lfs.DecodePointerFromFile(cwdfilepath)
-	if err != nil && !os.IsNotExist(err) {
+	if err != nil {
+		if os.IsNotExist(err) {
+			output, err := git.DiffIndexWithPaths("HEAD", true, []string{p.Name})
+			if err != nil {
+				LoggedError(err, tr.Tr.Get("Checkout error trying to run diff-index: %s", err))
+				return
+			}
+			if strings.HasPrefix(output, ":100644 000000 ") || strings.HasPrefix(output, ":100755 000000 ") {
+				// This file is deleted in the index.  Don't try
+				// to check it out.
+				return
+			}
+		} else {
 			if errors.IsNotAPointerError(err) || errors.IsBadPointerKeyError(err) {
 				// File has non-pointer content, leave it alone
 				return
@@ -78,6 +91,7 @@ func (c *singleCheckout) Run(p *lfs.WrappedPointer) {
 			LoggedError(err, tr.Tr.Get("Checkout error: %s", err))
 			return
 		}
+	}
 
 	if filepointer != nil && filepointer.Oid != p.Oid {
 		// User has probably manually reset a file to another commit

git/git.go

@@ -258,6 +258,23 @@ func DiffIndex(ref string, cached bool, refresh bool, workingDir string) (*bufio
 	return bufio.NewScanner(cmd.Stdout), nil
 }
 
+func DiffIndexWithPaths(ref string, cached bool, paths []string) (string, error) {
+	args := []string{"diff-index"}
+	if cached {
+		args = append(args, "--cached")
+	}
+	args = append(args, ref)
+	args = append(args, "--")
+	args = append(args, paths...)
+
+	output, err := gitSimple(args...)
+	if err != nil {
+		return "", err
+	}
+
+	return output, nil
+}
+
 func HashObject(r io.Reader) (string, error) {
 	cmd, err := gitNoLFS("hash-object", "--stdin")
 	if err != nil {

t/t-checkout.sh

@@ -51,6 +51,14 @@ begin_test "checkout"
   grep 'accepting "file1.dat"' checkout.log
   grep 'rejecting "file1.dat"' checkout.log && exit 1
 
+  git rm file1.dat
+
+  echo "checkout should skip replacing files deleted in index"
+  git lfs checkout
+  [ ! -f file1.dat ]
+
+  git reset --hard
+
   # Remove the working directory
   rm -rf file1.dat file2.dat file3.dat folder1/nested.dat folder2/nested.dat