This release of the Clover-for-IDEA plug-in supports the "external build" feature introduced in IDEA 12 official release (File > Settings > Project Settings > Compiler > "Use external build" toggle). However, in order to use the external build, please use the IDEA version 12.1.1 or later.
For older versions, i.e. a combination of Clover 3.1.8-3.1.12 and IDEA 12.0.0-12.1.0 please keep the "external build" feature disabled.
Open the File > Settings > Project Settings > Compiler page.
Use the following state for toggles:
The "Clover for IDEA" has been renamed to "Atlassian Clover for IDEA" on the plug-in list (File > Settings > Plugins).
See also the Clover-for-Ant Changelog.