Clover 3.1.11 also requires the "external build" feature disabled.
According to the information from JetBrains team, the IDEA 12.1 will have new API for handling source code transformations in the external build, so probably the next Clover release (3.1.12) will have support for it (CLOV-1186).
I'm happy to inform that Clover 3.1.12 supports the "external build" feature. It's necessary to use IntelliJ IDEA 12.1.1 or later. More details here:
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