Sorry, I've just been shooting from the hip because I don't use the NeoReader and I can't be bothered to pm enable it.
It could be that they never correctly implemented the file: scheme and that they only use the content: scheme.
Does this execute happily?
Code:
am start -a com.onyx.android.sdk.data.IntentFactory.ACTION_EXTRACT_METADATA -c android.intent.category.DEFAULT -d file:///sdcard/whatever.pdf