Thanks for Your reply.
I found in hts-log.txt the command webhttrack have used:

httrack -q -%i -w <http://www.scholarpedia.org> -O
/home/boris/Books/httrack//www.scholarpedia.org -n -%P -N0 -s2 -p7 -D -a -K0
-c4 -%k -A25000 -F "Mozilla/4.5 (compatible; HTTrack 3.0x; Windows 98)" -%F
"<!-- Mirrored from %s%s by HTTrack Website Copier/3.x [XR&CO'2008], %s -->"
+*.png +*.gif +*.jpg +*.css +*.js -ad.doubleclick.net/* -%s -%u -iC1 -iC1

I'd like to add two more options: "-n" and "-%I" (perhaps it'll make the wiki
searchable) and --continue the download. How it is possible?
I have lots of .tmp files left - but last time httrack said "Done. Ok"; Does
it mean - the download is not really finished?