Fix parse flags

Setting PARSE_IS_SYSTEM to the parse flags happens long after the
APK is actually parsed. So, we fail to pick up the boot aware and
protected storage attributes. Instead, always pull them from the
manifest, but, remove the flags if the package is not actually a
system package.

Also, we were incorrectly skipping certificate verification if
the flag PARSE_IS_SYSTEM was set. However, this flag is used for
_any_ system package -- whether it's physically on /system or if
it's an unbundled update. Instead, we should only skip this step
if the flag PARSE_IS_SYSTEM_DIR. We can implicitly trust any
APK actually stored in /system.

On a different note ... At some point, we will break apart the
parse flags into actual parse flags [i.e. those that change
physically parsing an APK] and policy flags [i.e. those that
change the interpretation of the APK contents].

Bug: 28116074
Bug: 28088617
Change-Id: I85246b0cb18fb5647df3618107910e288137fbc7