Force RubyMine to notice file system changes

If you did file operations inside a shell or for example using Nautilus Show archive.org snapshot , it can take quite a while until RubyMine takes note of them and updates things like your project tree or its internal file list.

Flushing file system buffers Show archive.org snapshot helps you out (run it from a terminal):
sync

This is also possibly via the RubyMine menus: File → Synchronize.