Given that the pom has a correctly configured scm tag section then it's just a case of finding the browsable file.
Normally mercurial repo's are exposed using hgweb.cgi or hgwebdir.cgi.
Not sure about hgweb - use hgwebdir myself - but - the trick is to grab the raw file version of the tip revision. Once continuum can grab this then it will use the scm tags to get the project.
When you run hg clone to grab the repository it will always check out the entire repository.
If you have a multi-module project - check out the root pom, set for non-recursive checkout and make sure that you don't set --non-recursive for the maven build. Otherwise you will end up with an identical build set for each child pom (a copy of the parent).