In Automator, all the repositories from a datasource (SCM, MLS, etc) share the same run configuration, but sometimes you need to run some of the repositories with a different one.
For instance, I havie set of repositories to analyze but in one of them, I only want the analysis of some of its directories.
git://xenbits.xen.org/xen.git
git://xenbits.xen.org/osstest.git
git://git.kernel.org/pub/scm/linux/kernel/git/torvalds/linux-2.6.git - arch/*/xen arch/*/include/asm/xen drivers/xen drivers/*/*xen* include/xen arch/*/pci/*xen*
Automator should support this feature.