We are attempting to turn our site into a static copy to host externally.  In
testing we run into a problem where httrack sometimes changes the files to
html instead of their native type.

so we will get
link type="text/css" rel="stylesheet" href="modules/user/user.html?e"

instead of
link type="text/css" rel="stylesheet" href="modules/user/user.css?e"

Not sure why it is replacing the type and only doing it some runs instead of
others.  

HTTrack version 3.48-22
Command:
httrack -%F "" "<site>" -O "<folder>" -s0 +*.css +*.js <fileTypes>
-www.google-analytics.com/* -*.com/*  -*/* +www.<site>.com/* -c32 -N
"%h%p/%n.%t" --disable-security-limits --max-rate 999999 -q --ext-depth=0

#-%F                    Remove Footer with timestamp
#-O                     Specify output location
#-s0                    ignore robots.txt
#+*.css *.js            Include these file types and map to new location
#-www.google            Don't download data from site - keep as a link to that
site
#-*.com -*/*            In fact don't download from any external sites.
#+www.a-p.com/*         now that other sites are excluded, add back our site.
#-c32                   Max number of connections / simultaneous downloads
#-N "%h%p/%n.%t"        Specify format of file
#       %h%p            host and path
#       %n.%t           file name dot file extension.     %N removes the dot,
don't use.  aka indexhtml
#--disable-security-limits            Ignore max connection speed in httrack
#--max-rate             Specify max connection speed. 
#-q                     quiet mode, no questions.  needed to run as a script.
#-ext-depth             Its supposed to prevent crawls of external sites. 
Doesn't work by itself