As explained in my last post, I’m moving from a Fusecompress 2.0 backend to the more stable 0.9.x branch.  I’m using the following code to move the repository, incrementally (and in recoverable way).  The disk is too small to maintain both copies at once.  Because the normal tools (mv/cp/rsync) work depth-first and daily.0 is nearly identical to daily.1 (and daily.2, etc.), only a small amount of space is freed after moving daily.0 and the disk eventually fills.

As with everything posted here, use this at your own risk and ALWAYS backup!

dest=/home/backup.new/snapshot
source=/home/backup/snapshot

# Create the directories
find . -type d -print0 | while read -r -d '' file
  do
  if test ! -d "$dest/$file"
    then
      mkdir -vp "$dest/$file"
      touch --reference="$file" "$dest/$file"
      chown --reference="$file" "$dest/$file"
  fi
done

# Move the files in, link any duplicates, and remove the original.
for ssnap in `ls $source`
  do
  cd $ssnap
  find . ! -type d -print0 | while read -r -d '' file
    do
    if test ! -e "$dest/$ssnap/$file" -o -h "$dest/$ssnap/$file"
      then
        cp -adnvp "$file" "$dest/$ssnap/$file"
      else
        echo "$dest/$ssnap/$file" exists.
    fi
    for dsnap in `ls $source`
      do
      if test "$ssnap" = "$dsnap"
        then continue
      fi
      echo "Checking $dsnap - ../$dsnap/$file"
        if test "$file" -ef "../$dsnap/$file";
        then
          ln -v "$dest/$ssnap/$file" "$dest/$dsnap/$file"
          rm -vf "../$dsnap/$file"
        fi
    done
    rm -vf "$file"
  done
done

Updated 2012-01-03: Filenames/Directories names with new line character caused mischief. Fixed by null separating.  Also included symlinks, char devices, and other special filetypes in the transfer.