There is currently no way to restrict workflow triggers in a project to specific repositories.
Someone commits a fix with a comment such as "Implementing JIRA-12345 workaround until CORECOMPONENT-123 is fixed"
Both issues would be automatically transitioned to 'In Progress' by this comment, even though no one is actually working on CORECOMPONENT-123.
It would be great to allow auto-issue transitions to be configured / restricted by repositories.
This is the customer facing issue for https://jdog.jira-dev.com/browse/FUSE-2786.