You usually remember to do that anyway after you've been trying to track down a bug on a line of JavaScript that Webstorm says doesn't exist for the last two hours.
There's a feature in the context-menu for manually synchronising directories with their real filesystem equivalent, but this shouldn't be necessary and is annoying to do. If you have an external tool acting on your project (such as a gulp task or a third-party Git client), what you see in the file browser or in open tabs becomes out-of-date. The Java wrapper around the filesystem doesn't actively watch for file changes (by, for example, using the fsevents api on OS X), and as a result can become easily desynchronised from the actual filesystem.
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