P.S. I've read the query string rewrite notes, but they seem to only apply to
controlling how the part of the file name after the .php? | .asp? |.cfm? is
rewritten.  Since I'm mirroring thousands of sites, and don't know what the
string will be before the ?, this only seems to fix part of the problem.  I'm
using Linux, so file name legality is not an issue, I'm able to manually save
file names like 

<http://www.matthewmarks.com/index.php?n=1&a=123&im=1>

so am just trying to get httrack to do the same for both href values and
files.