We are trying to integrate bamboo with stash, but the workflow between stash and bamboo is currently not crystal clear.
First, build status seems to not appear in stash, so I'm not sure if there is a setup problem somewhere (applications links seems to be correctly setup, as well as notifications from bamboo).
But the first thing we are not sure is that bamboo seems to be able to automatically trigger a build after commits have been done to a branch. So questions are:
Assuming you have branch builds setup and the build status is being published to Stash you should be able to stop pull requests being merged unless they have a green build.
There is a setting on the Pull Requests tab in repository settings to control the merge behaviour.
Hope that helps,
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