Subprocess error handling: Initialise $? to -1

When system(3perl) fails due to syscall error, it sets only $!.  When
it succeeds it sets only $? and sometimes trashes $!.  Conversely,
close of a popened filehandle always sets both in all cases.

Document this in a comment.

So when using system and relying on $?/$! (rather than looking at
system's return value), such as when about to use failedcmd, it's
necessary to initialise $? to -1.

Fix the three call sites where system might be followed by failedcmd
but this wasn't done.