Calls to `shell` in boot.sh bash scripts cause command not found errors

There's this sort of thing in a couple of the boot.sh scripts:

EXE=""
if [[ $(shell uname -s | grep -c 'MSYS\|MINGW') -eq 1 ]]
then
  EXE=".exe"
fi

This is causing a lot of command not found errors when running nofib for me using shake.

My best guess is that this code was copied from a Makefile where shell means something, but now these lines are in bash scripts, where shell isn't defined.

I'll make an MR momentarily