[Runtime] Teach BridgeObjectBox::retain() not to drop the "not native" bit.
The "not native" bit in a BridgeObject is important, because it tells
us when we need to go through the Objective-C -retain method
vs. swift_retain. Losing the bit means that swift_retain() will stomp
on some memory within an Objective-C object, thinking its the inline
reference count.
Co-debugged with Arnold, who then found where this bit was getting dropped.
Fixes rdar://problem/39629937.