This should be a simple enough concept, separate all key components in their own folders: directories like: includes, images, bin, info, documents, stylesheets, scripts, etc. You get the idea, what a nightmare to have your entire application in one folder, yikes! Furthermore, for stronger security measures, never place your site's folder in your server's root folder.
Also working with a source code control software such a Microsoft's Visual Source Safe goes a long way in protecting code. Many editors available now from HomeSite to Dreamweaver integrate this. Furthermore, Source Safe promotes versioning as well, just like .NET.
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