Plan branches break after a YAML Specs publish

Issue Summary

Plan branches break after a YAML Specs publish.

Steps to Reproduce

1. Create a Linked repository with your personal code. We'll call this linked repository "InnerRepo".
2. Create a build plan and configure InnerRepo in the build plan.
3. Export the plan to Yaml Specs.
4. Create a new repository in Bitbucket and host this Yaml export. We'll call this repository YamlRepo.
5. Create a branch in InnerRepo.
6. Create (in some way) a plan branch that points to the new branch.
7. Make a change in the Yaml file and publish the changes through Specs/RSS.

Expected Results

The plan branch will continue pointing to the repository branch.

Actual Results

The branch plan will point to master (or to the default branch that InnerRepo was configured to use).

Notes

Bamboo suffers from two limitations in the process:

Yaml Export

When a YAML export is made, Bamboo doesn't explicitly mention InnerRepo in the checkout task. This means that, when imported, Bamboo will use YamlRepo instead, thus breaking the pipeline.

Order in repositories.

If InnerRepo is explicitly mentioned, upon Specs publishing Bamboo will create both YamlRepo and InnerRepo, but YamlRepo will be first in the list (main repository). Thus the plan branching schema will use YamlRepo. This will break the pipeline too.

Workaround

Merge YamlRepo and InnerRepo into one repository would make this feature work properly.

Yaml configuration will diverge too, so if the Yaml file is updated on master, then those changes will need to be propagated accordingly.