The generated patch was missing a line of the diff.

The generated patch was missing a line of the diff.
genpatch was also depending on the new files being listed first by
'cvs diff' (which is the case but I'm not sure there is any hard
guarantee).
Use 'perl -w' for more checking, fix the resulting 'undefined value'
warnings. In many cases we don't just want $options{xxx} to exist, we
want it to be defined.
Restrict the scope of variables and remove unneeded variables.