Fix hardlink issue with whiteout deletes in the merge snapshotter.

Whiteouts may share the same inode which cause the snapshotter
to attempt to create a hardlink between two whiteouts in the destination layer.

The problem is that the first whiteout is only created if it is part of the lower layer from the base snapshot.
Otherwise, the whiteout is not created in the destination layer because it is not needed.

If the first whiteout is not created in the destination, attempting to create a hardlink for the second whiteout will fail.

To avoid this issue, this fix disables hardlinks for whiteouts.

Signed-off-by: Grégoire Payen de La Garanderie <gregoire.payen.de.la.garanderie@intel.com>

client/mergediff_test.go

@@ -428,6 +428,33 @@ func diffOpTestCases() (tests []integration.Test) {
 			),
 		})
 
+		// Check that deleting together a file from the base and another one from a merge
+		// does not result in a crash.
+		deleteFileAfterMergeCmds := []string{
+			"rm /unmodifiedDir/deleteFile1 /unmodifiedDir/deleteFile2",
+		}
+
+		extraContent := llb.Scratch().
+			File(llb.Mkdir("/unmodifiedDir", 0755)).
+			File(llb.Mkfile("/unmodifiedDir/deleteFile2", 0644, []byte("foo")))
+
+		tests = append(tests, verifyContents{
+			name: "TestDiffDeleteFilesAfterMerge",
+			state: llb.Diff(
+				base(),
+				runShell(llb.Merge([]llb.State{
+					base(),
+					extraContent,
+				}),
+					joinCmds(
+						deleteFileAfterMergeCmds,
+					)...)),
+			contents: mergeContents(
+				apply(
+					fstest.CreateDir("/unmodifiedDir", 0755)),
+			),
+		})
+
 		// Opaque dirs should be converted to the "explicit whiteout" format, as described in the OCI image spec:
 		// https://github.com/opencontainers/image-spec/blob/main/layer.md#opaque-whiteout
 		opaqueDirCmds := []string{

snapshot/diffapply_unix.go

@@ -724,7 +724,10 @@ func (d *differ) overlayChanges(ctx context.Context, handle func(context.Context
 				return errors.Errorf("unhandled stat type for %+v", srcfi)
 			}
 
-			if !srcfi.IsDir() && c.srcStat.Nlink > 1 {
+			// Changes with Delete kind may share the same inode even if they are unrelated.
+			// Skip them to avoid creating hardlinks between whiteouts as whiteouts are not
+			// always created and may leave the hardlink dangling.
+			if !srcfi.IsDir() && c.srcStat.Nlink > 1 && c.kind != fs.ChangeKindDelete {
 				if linkSubPath, ok := d.inodes[statInode(c.srcStat)]; ok {
 					c.linkSubPath = linkSubPath
 				} else {