Currently, unless you tweak the maven configurations on the build agents to reflect the way that atlas-compile or atlas-package work, the only reasonable way to have Bamboo build custom Atlassian plugins is to manually install the SDK, then use a command task to call directly to atlas-compile, atlas-package, etc.

It would be great to be able to install the Atlassian SDK through the plugin manager and have that expose the appropriate tasks for plugin developers. This would then allow a simple mechanism for keeping the SDK up to date within the Bamboo agents via the UPM.