Rather than a detailed review, just one thing that caught my eye...

   foreach (@$files) {
      $table{$_} = substr $_, 0, -2;  
   }
[download]

In this loop, the
    $table{$_} = substr $_, 0, -2;
statement seems intended to snip the extension off the path/filename of a C source file and associate the file name so truncated with the original, full name. It assumes the extension is always two characters, e.g., '.c'. It's not a bad assumption in this case, but of course immediately fails in the face of extensions like '.cc', '.cpp', etc., leaving one with a perhaps very puzzling bug — but of course, this will never happen! Whenever I encounter an assumption like this, old scars begin to throb and I feel a strong urge to program defensively.

Assuming one does not want to use well-tested and platform independent CPAN modules for manipulating file names, one might write something like (untested)
    for my $file_name (@$files) {
        (my $base_name = $file_name) =~ s{ [.] [^.]* \z }{}xms;
        $table{$file_name} = $base_name;
        }
which snips off the last '.whatever' extension regardless of its length, and, even though more verbose, has, I feel, a certain 'self-documentation' quality.

Update:

    `gcc $_ -o substr $_, 0, -2` foreach (@$files);
I couldn't get it to work syntactically... clarity is sacrificed... Is something like this even possible?

I agree with your concerns about clarity, but in any event, one way might be something like this (of course, you would use qx{...} instead of print qq{...}):

>perl -wMstrict -le
"print qq{gcc $_->[0] -o $_->[1]}
   for
     map [ $_, s{ [.] [^.]* \z }{}xmsr ],
     qw(see cee. foo.c foo/bar.cc foo/bar/baz.cpp)
     ;
"
gcc see -o see
gcc cee. -o cee
gcc foo.c -o foo
gcc foo/bar.cc -o foo/bar
gcc foo/bar/baz.cpp -o foo/bar/baz
[download]

(Prior to 5.14 and the introduction of the  //r regex modifier, you can use
    map { (my $o = $_) =~ s{ [.] [^.]* \z }{}xms;  [ $_, $o ] }
instead.)

Further Update: Or even:

>perl -wMstrict -le
"print qq{gcc $_ -o @{[ s{ [.] [^.]* \z }{}xmsr ]}}
   for qw(see cee. foo.c foo/bar.cc foo/bar/baz.cpp);
"
gcc see -o see
gcc cee. -o cee
gcc foo.c -o foo
gcc foo/bar.cc -o foo/bar
gcc foo/bar/baz.cpp -o foo/bar/baz
[download]

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