Make sure you have option Synchronize files on frame activation = ON (that's so by default). In project view, under source root expand some directory which you are planning to perfrom external changes in. Open modal dialog (tested Refactor / Rename, Build jars, Analyze code). Switch to external file manager. Copy some new files to your project directory. Tested image files, java source. Switch back to IDEA. Close modal dialog. Result: synchronization does not happen. New files are not shown in project view, and compiler does not process them. On main menu | File | Synchronize the synchronization works Ok.