You can use the "synchronize" button (two yellow arrows) or in short Ctrl+Alt+Y
Click File>Synchronize (or) shortcut ctrl+Alt+Y
I know this question was posted a few years ago, but maybe this info will help someone in the future. I was actually looking into a similar issue, and doing the following worked for me:
Go to Settings > Build, Execution, Deployment > Compiler and make sure "Make project automatically" is checked.
Right click on your Project in the left pane and click on "Synchronize"
You can see the status in the round circling icon at the bottom left of the IDE
Intellij can highlight variable instances, you just need to enable it . Further, if you invoke compile project, Intellij will just compile changed files (and hotswap when possible, if you are in debug mode & deploying to e.g. tomcat)
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