stgit truncates binary files to zero length when applying patches

When applying patches and not fast-forwarding, stgit truncates the binary files to zero length:

  $ cg-init .
  defaulting to local storage area
  Committing initial tree 4b825dc642cb6eb9a060e54bf8d69288fbee4904
  Committed as 73161b6ee428ac8b1c1b16b560c40e13330693d2.

  $ stg init

  $ stg new foo
  Invoking the editor: "emacs .stgit.msg"... done (exit code: 0)

  $ cp /bin/bash .

  $ stg add bash

  $ stg refresh
  Refreshing patch "foo"... done

  $ ls -l
  total 584
  -rwxr-xr-x  1 kha vtech 593304 Nov 15 15:34 bash*

  $ stg pop
  Popping patch "foo"... done
  No patches applied

  $ stg new bar
  Invoking the editor: "emacs .stgit.msg"... done (exit code: 0)

  $ echo bar > bar.txt

  $ stg add bar.txt

  $ stg refresh
  Refreshing patch "bar"... done

  $ stg push foo
  Pushing patch "foo"... done
  Now at patch "foo"

  $ ls -l
  total 4
  -rw-r--r--  1 kha vtech 4 Nov 15 15:34 bar.txt
  -rwxr-xr-x  1 kha vtech 0 Nov 15 15:35 bash*

Without the "bar" patch, popping and then pushing "foo" works as expected.