A heads up for every one in case you encounter the same problem as I did. It
seems there is a minor bug when using the assume option in a custom .httrack
file when running httrack from the command line.

I initially had it set as follows:

#Mime types assumptions
set assume "php=text/html,php3=text/html,php4=text/html,asp=text/html"

However it appears that the first equal sign gets removed when the .httrack
file is parsed (resulting in the option not working). Also it seems that the
stringing of multiple parameters in one line does not work for this option. I
ended up getting it working using the following syntax:

#Mime types assumptions
set assume="php=text/html"
set assume="php3=text/html"
set assume="php4=text/html"
set assume="asp=text/html"

The first equal sign gets stripped out by the parser keeping the second one
(which is required) and placing one entry per line solves the other issue.