have IntelliJ IDEA refresh the project and detect changed files

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)

You can use the "synchronize" button (two yellow arrows) or in short Ctrl+Alt+Y

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