Test Clover against IntelliJ IDEA 2016.3 EAP (build 163.5219.11), released on Sep 28, 2016.
1) In IDEA 2016 the Preferences dialog (on OSX - IDEA -> Preferences, on Linux/Windows - File > Settings) does not show "Clover (project settings)", we see the "Clover (global settings)" only.
Workaround: open on the 'Cloverage' view, click 'Filters' button. It opens the "Clover (project settings)" dialog with the 'Filters' tab preselected; it's possible to switch to other tabs as well.
2) The "Clover (global settings)" is assigned to the "Other Settings" category. Consider moving it to the "Build, Execution, Deployment" (in this category is placed the IDEA's "Coverage" plugin).
moved both "Clover (project settings)" and "Clover (global settings)"
3) Colour pickers have white checkboxes instead of showing the current colour:
fixed and improved - replaced by JPanels: