Use $(...) notation for subshells in system tests

The changes were mostly done with sed:

find . -name '*.sh' | xargs sed -i 's/`\([^`]*\)`/$(\1)/g'

There have been a few manual changes where the regex wasn't sufficient
(e.g. backslashes inside the `...`) or wrong (`...` referring to docs or
in comments).

bin/tests/system/rsabigexponent/ns2/sign.sh

@@ -20,7 +20,7 @@ outfile=example.db.bad
 for i in Xexample.+008+51650.key Xexample.+008+51650.private \
 	 Xexample.+008+52810.key Xexample.+008+52810.private
 do
-	cp $i `echo $i | sed s/X/K/`
+	cp $i $(echo $i | sed s/X/K/)
 done
 
 $SIGNER -g -s 20000101000000 -e 20361231235959 -o $zone \