Restore checkObjectCollisions flag

Restore checkObjectCollisions flag

I am developing an offline pack verification feature based on
PackParser. The birthday collision check is a prohibitive obstacle
to performance at scale because it interacts with the repository
to perform collision checks. This CL restores the checkObjectCollisions
flag that was removed in 9638e0aa87614a6fb4f109bbeac0cde3462b9769,
while changing the flag getter and setter to protected from public as a
precaution against misuse.

Change-Id: I363cd0c9de57c5e8659cdfe2d51b17823f4fe793
Signed-off-by: David Pletcher <dpletcher@google.com>