Tracking channel 20ms integration WIP
Update file end after write to file log.
Flatten out manage acq state machine.
Removed acq_manage structure, replaced by locals in manage_acq().
Squash acq load into a single blocking call.
Swap acq_start and acq_wait_done for a blocking acq_search.
Flattened acquisition state machine.

This involves a nasty hack with thread priorities to deal
with the interrupt not being cleared until the next write
to the nap acq init register.  This should be changed in the
nap to clear the interrupt when the interrupt register is read.
Rework to use new FFT acquisition core.
Use semaphore to wake up nap exti thread.  Fixes a race condition.
Use mutex for to lock SPI bus.  Fixes priority inversion problem.
Allow blocking acqusition to timeout and retry timing strobe when it does.
Fix restarting of acquisition search.
Add wait for timing strobe.
Read acqusition parameters from FPGA configuration and use instead of hard coded constants.

Remove parameters for code phase search, no longer needed.
Merge branch 'coffee_fix' of github.com:gsmcmullin/piksi_firmware
Merge branch 'thread_sync' of github.com:gsmcmullin/piksi_firmware
Merge branch 'fft_acq' of github.com:gsmcmullin/piksi_firmware into fft_acq
Fix acquisition code phase.
Use the new fixed baseline method (doesn't drop to float when adding a
sat).
Change to using the new tracking loops with FLL aiding.