How can I make a link to a git changeset in Trac when there is more than one repository and neither one is default?

If your repository is named repo, you can link to the changeset with [changeset:af54b6d/repo].

I am using subversion, but asuming git changeset links work the sam way, you should use repo:changeset:af54b6d, where you must define repo in the [intertrac] section of the trac.ini. See also InterTrac