Run shellcheck on script files

Run shellcheck on script files

Run using:

for file in $(find . -not \( -path ./subprojects -prune \) -name "*.sh")
do
realfile=$(realpath "$file")
shellcheck --norc --format=diff --shell sh
--enable=add-default-case,avoid-nullary-conditions,check-unassigned-uppercase,deprecate-which,quote-safe-variables
"$realfile"| patch "$realfile"
done
exit

Plus manual edits.