Use AX_PTHREAD macro to initialize pthread, move up in configuration order.

ODE now requires pthread, so it must appear before ODE in the
configuration order.
Upgrade to ODE 0.13.1.

No more special flags needed during configure.
Upgrade to liblo-0.28
Add maintainer mode and silent rules to autotools.
Disable silent rules and use debug mode by default, allow it to be disabled during autogen.
Remove extra add_simulation() call for visual/haptics connection.
Use a semaphore to synchronize thread initialization.

Without this, Phantom library fails to start correctly -- apparently a
race condition, since it doesn't fail when a debugger or strace slows
down execution.