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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. 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. It should be noted though that this is easily remedied by going to File/Settings/System Settings and checking the "Synchronize Files on frame or editor tab activation" option. Designed for productivity, IntelliJ IDEA delivers a remarkable return on investment (ROI).
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It's also recommended to more explicitly represent your workflow within WebStorm itself. According to a recent Forrester Consulting study, a company’s investment in IntelliJ IDEA can pay for itself in less than 3 months, and has an ROI of 628 on average over 3 years.
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Most external tools/tasks can be handled with WebStorm. And if it's not in a plug-in, then you can handle it with the File Watchers.
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