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.
Non-native filesystem causes issues 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. For casual, unsophisticated applications by someone who grew up with green screen character based computers, it's probably OK. For this reason, I would not recommend Emacs to anyone who is under 50 year old, or who needs power user capabilities. The things I just mentioned, are all present in some limited and inept form, but falls far short of current standard of good user interface design. To this day, it lacks or struggles with very basic things, like interactive dialogs, toolbars, tabbed interface, file system navigation, etc., etc. So Emacs does 5% or what an editor should do quite will, and is surprisingly under-powered and old fashioned at the other 95%. Unfortunately, it didn't keep up with the times and fails to take advantage of the entire world of GUI design that's revolutionized computer science since then. In fairness to Emacs, its original design was conceived in that context and is rather good at some things, like flexible ability to bind commands to keyboard shortcuts. User interface is terrible I was using Emacs in the early 1980's, before there were GUIs.
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