For automatic branch detection Bamboo assumes that a user has organized his repository this way:

/project-a/trunk
/project-a/branches
/project-a/tags
/project-b/trunk
/project-b/branches
/project-b/tags

This is pretty standard and works fine with automatic branch detection in Bamboo 4.2. The user can set the repository location to /project-a/trunk, and it will look for branches in /project-a/branches. However, users have been considering an alternate repository layout that looks like this:

/trunk/project-a
/trunk/project-b
/branches/<branch-name>/project-a
/branches/<branch-name>/project-b

This would allow him to create a branch that encompasses multiple related projects, all of which will be modified together in that branch, instead of creating separate but inter-dependent branches under each project's own trunk/branches/tags structure.

However, this structure doesn't work well with Bamboo. The user can configure it to look for branches of project-a under /branches, but then Bamboo thinks /branches/<branch-name> is a branch of project-a. In reality, the branched version of project-a is one level deeper at /branches/<branch-name>/project-a.