With recent changes that have been made to the openjfx 9-dev repository, IntelliJ does not quite know about all relevant source code that needs to be available to successfully develop and run JavaFX applications from within IntelliJ. The small patch below adds the missing directories into the IntelliJ-specific files for javafx.base and javafx.graphics modules.

diff --git a/.idea/base.iml b/.idea/base.iml
--- a/.idea/base.iml
+++ b/.idea/base.iml
@@ -9,6 +9,7 @@
       <sourceFolder url="file://$MODULE_DIR$/modules/javafx.base/src/test/java" isTestSource="true" />
       <sourceFolder url="file://$MODULE_DIR$/modules/javafx.base/src/test/resources" isTestSource="true" />
       <sourceFolder url="file://$MODULE_DIR$/modules/javafx.base/src/main/java-jfr" isTestSource="false" />
+ <sourceFolder url="file://$MODULE_DIR$/modules/javafx.base/build/gensrc/java" isTestSource="false" />
       <excludeFolder url="file://$MODULE_DIR$/modules/javafx.base/build/classes" />
       <excludeFolder url="file://$MODULE_DIR$/modules/javafx.base/build/dependency-cache" />
       <excludeFolder url="file://$MODULE_DIR$/modules/javafx.base/build/libs" />
diff --git a/.idea/graphics.iml b/.idea/graphics.iml
--- a/.idea/graphics.iml
+++ b/.idea/graphics.iml
@@ -11,6 +11,8 @@
       <sourceFolder url="file://$MODULE_DIR$/modules/javafx.graphics/build/resources/jsl-prism" isTestSource="false" />
       <sourceFolder url="file://$MODULE_DIR$/modules/javafx.graphics/src/test/java" isTestSource="true" />
       <sourceFolder url="file://$MODULE_DIR$/modules/javafx.graphics/src/test/resources" isTestSource="true" />
+ <sourceFolder url="file://$MODULE_DIR$/modules/javafx.graphics/build/gensrc/jsl-prism" isTestSource="false" />
+ <sourceFolder url="file://$MODULE_DIR$/modules/javafx.graphics/build/gensrc/jsl-decora" isTestSource="false" />
       <excludeFolder url="file://$MODULE_DIR$/modules/javafx.graphics/build/classes" />
       <excludeFolder url="file://$MODULE_DIR$/modules/javafx.graphics/build/dependency-cache" />
       <excludeFolder url="file://$MODULE_DIR$/modules/javafx.graphics/build/libs" />