BPEL migration, SCM, and BPEL builds

We've got 10.1.2.0.1 bpel sources in SCM and want to migrate them (without too much overhead) to 10.1.3.1. We frequently encounter the build warning for newly migrated projects:
Warning: bpel.xml file not found at <project dir>\bpel\bpel.
Not sure where the extra layer is coming from. I'm scouted the jpr file and don't see it but I guess it's possible an environment variable is already carrying the directory level.
Any ideas on what this is all about?

Looks like it is the application jws file defining the additional layer. Once removed it is fine.

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