@ashley reported that using extension.json in 1.25 with manifest_version set results in:
[15-Jun-2015 19:18:02] PHP Warning: array_merge_recursive() [<a href='function.array-merge-recursive'>function.array-merge-recursive</a>]: Argument #1 is not an array in D:\\xampp\\htdocs\\shoutwiki\\trunk\\includes\\registration\\ExtensionProcessor.php on line 294
We should make sure that manifest_version at the very least does not cause warnings in 1.25.