[TYPO3-core] Extensions automatically removed in PackageStates.php causing fatal errors

[Peter Beernink]

Hi,

After upgrading a project from TYPO3 6.2b1 to the latest master I fatal 
errors about extensions not being loaded anymore.
This is because most extensions are automatically removed from the 
PackageStates.php

When resetting the PackageStates.php to 'beta1' and removing the 
typo3temp/Cache the first page hit works correctly, but the second one 
gives an error like

BadFunctionCallException: TYPO3 Fatal Error: Extension key "phpunit" is 
NOT loaded! in 
/....../typo3_src/typo3/sysext/core/Classes/Utility/ExtensionManagementUtility.php 
on line 104

I have traced this issue to commit a71add78 (issue 52828), but I'm not 
sure if this is a breaking change for which I need to modify the 
extensions or that a bug has been introduced in this change.

Greets,
Peter