The workspace is created before the Pre-SCM plugin executes, so the build never fails. If no pre-existing clone exists our script will make one as needed (it also knows the repository URL).

An extreme pity this is seen as a special case considering it worked perfectly fine in the past.

I see two possible solutions:
1) Have an absolute last resort possibleQualifiedBranches entry of singleBranch - ie. totally unmodified from the specification passed to it in the build configuration.

2) Consider the case of "refs/*" to always be properly qualified.

Which one do you prefer?

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