Timer code rework. Done so far:

 o Fix interrupt handler to not loose cycles
 o Warn about lost interrupts.
 o Fix calibration of the R4000 CPU timer.

Still to do:
 o General cleanup of the timer code
 o Microsecond timers for the Indy
 o The calculated values for r4k_offset are still off by ~480 from the
   theoretical values.  That means we're going to loose about 46 s per
   day.  Are the crystals that bad or is there still a bug hidden
   somewhere?  Maybe an option to set r4k_offset to a user supplied
   value might help?
 o Handle lost interrupts more gently so we don't loose time.
 o Handle 100MHz R4000 count / compare bug.

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