There is some support in there for build-time changing of things. A file, .markdownsite.yml, can be read in and do things like change where the directory containing markdown files, or the webroot is, and will switch branches. Definitely a place that could be expanded — if you take a look at Manager/lib/MarkdownSite/Manager/Plugin/Maker.pm you’ll see how it builds. So maybe some of that can fit in, and alternative builders are certainly something to think about.
As far as git hooks, right now, you could add one to make your site import with the following:
A githook could trigger an import with curl, for example:
curl -XPOST -d'repo=git@github.com:symkat/mds-example.markdownsite.net.git' https://markdownsite.com/import
The first run will make the site and assign a domain, subsequent runs update the same domain.
Thanks for checking it out and your feedback, definitionally given me some things to think about!