<p>Is there a tool that creates a diff of a file structure, perhaps based on an MD5 manifest. My goal is to send a package across the wire that contains new/updated files and a list of files to remove.  It needs to copy over new/updated files and remove files that have been deleted on the source file structure?</p>

You might try rsync. Depending on your needs, the command might be as simple as this:
```
```
rsync -az --del /path/to/master dup-site:/path/to/duplicate
```
```
Quoting from
rsync's web site
:
rsync is an open source utility that
  provides fast incremental file
  transfer. rsync is freely available
  under the GNU General Public License
  and is currently being maintained by
  Wayne Davison.
Or, if you prefer
wikipedia
:
rsync is a software application for
  Unix systems which synchronizes files
  and directories from one location to
  another while minimizing data transfer
  using delta encoding when appropriate.
  An important feature of rsync not
  found in most similar
  programs/protocols is that the
  mirroring takes place with only one
  transmission in each direction. rsync
  can copy or display directory contents
  and copy files, optionally using
  compression and recursion.