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Added an optional active_installs field. This should be an positive integer that indicates how many sites use your plugin. WordPress will show it in the "view version 1.2.3 details" pop-up. For example, if you set it to 10000, users will see "Active Installs: 10,000+".
Added automatic directory structure validation. This should help developers identify and fix issues caused by putting all plugin files at the root of the update package. See acb8476 for more details.
The update checker will no longer inadvertently trigger autoloading when calling class_exists(). Apparently, some autoloader implementations will throw warnings or even crash if they get a class name that they can't load.