Makefile: replace $fatal with $stop to avoid verialtor stopped during eval without providing snapshots

modify Emulator::execute function argument list from (uint64_t n) to (uint64_t max_cycle, uint64_t max_instr)

Log and waveform are controlled by cpu clock cycles instead of simulated cycles.
When loading from snapshot and assert stops the simulation, we cannot know the accurate cpu cycle.
To determine the actual cpu clock, we print cycleCnt when loading from snapshot.

We need to asynchronous reset the system when reset is true.
In verilator model, it's done by always resetting the external devices when reset is true.
After the reset signal is released, we call init once for external devices to make sure they are correctly reset.

This reverts commit 118846bd.

* lr_valid will be copied from processor to emulator when:
    * sc falied &&
    * processor's lr_valid is set to false &&
    * emulator's lr_valid is set to true

* It will make snapshot more precise
* NEMU that includes commit d4efeb7 is needed to use difftest