Arduino.h not found when selecting run configuration "upload"

[AlexSchmid22191]

After upgrading to the latest CLion 2016.3.2 and installing the CLionArduinoPlugin 1.2.3 the IDE no longer finds the Arduino.h, i.e. it displays Arduino.h not found. Inbuilt Arduino specific functions like digitalRead produce the warning "Can't resolve the variable digitalRead". However, this happens only while the run configuration upload is selected. When selecting "build all", Arduino.h gets properly found. Nevertheless, the sketch can still be uploaded with the upload configuration, despite the displayed error messages.

[ghost]

I'm having the same issue with 2017.2 and 1.2.3 of the plugin. Also the -size behaves the same way.