$answer .= s/^-/\t-/gmr . "\n" for /\S.*?(?= +-)/g;

This leaves out the  -tag 2 at the very end of the c.l. string. Changing the look-ahead to  (?=(?: +-|$)) fixes this:

c:\@Work\Perl\monks>perl -wMstrict -le
"$_ = q(execute test_number_1 -tex -tex_args -sub_args +debug_dir=./ -
+sub_args +debug_dir=./ -constraint parity_en,random_en -sub_args '\"'
+ ruck=1 '\"' -constraint dual_en -sub_args -cd -sub_args 2596.slow -s
+ub_args test -seed 1 -tex_args- -opt 1 -tag 2);
 ;;
 print qq{$_ \n};
 ;;
 my $answer = '';
 $answer .= s/^-/\t-/gmr . \"\n\" for /\S.*?(?=(?: +-|$))/g;
 $answer =~ s{^(\s*)(-\w+)\n\K((?:.*\n)*?)(?=\1\2-\n)}
             { $3 =~ s{^}{\t}gmr }gem;
 ;;
 print $answer;
"
execute test_number_1 -tex -tex_args -sub_args +debug_dir=./ -sub_args
+ +debug_dir=./ -constraint par
ity_en,random_en -sub_args '"' ruck=1 '"' -constraint dual_en -sub_arg
+s -cd -sub_args 2596.slow -sub_args test -seed 1 -tex_args- -opt 1 -t
+ag 2

execute test_number_1
        -tex
        -tex_args
                -sub_args +debug_dir=./
                -sub_args +debug_dir=./
                -constraint parity_en,random_en
                -sub_args '"' ruck=1 '"'
                -constraint dual_en
                -sub_args
                -cd
                -sub_args 2596.slow
                -sub_args test
                -seed 1
        -tex_args-
        -opt 1
        -tag 2
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I still don't like that the  -cd is separated from its preceding  -sub_args argument. Have to think about that...