Use length of file instead of length of change for the dirstate entry.
+ hg init
+ hg add a
+ hg commit -m test -d 0 0
+ hg clone . ../b
a
+ hg verify
checking changesets
checking manifests
crosschecking files in changesets and manifests
checking files
1 files, 1 changesets, 1 total revisions
+ hg clone -U . ../c
cat: a: No such file or directory
+ hg verify
checking changesets
checking manifests
crosschecking files in changesets and manifests
checking files
1 files, 1 changesets, 1 total revisions
+ hg clone ../a
+ hg cat a
a