Fix all remaining issues reported by Verible lint.
It turns out that #965 undid some of the fixes in `ibex_alu.sv`
that were done in #980 around the `SHUFFLE_*`/`FLIP_*` signals.
Simple system is a basic verilator top-level testbench for running
executables. It has functionality for outputting text to a log file
and for the software to terminate the simulation