foreach my $line (<MAKFILE>) {
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I personally believe you should know that almost always in Perl (5) the Right™ way to iterate over the lines of a file is a while loop. You should also be using lexical filehandles.

        if ($line =~ m/SOURCE=\.\\(.*)$/i) {
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I generally chomp too, but incidentally $ matches right before \n too; you may also push the return value of the match operator.

    $fileLst = join " ", @fileLst;
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Perhaps you prefer to be explicit, and I'm sure many people would say that you're right, but there's a very convenient shortcut for join " ", @fileLst, which is "@fileLst"; also, I see no reason to create an intermediate temporary variable just to return it.

All in all, I will give you an example subroutine which will accept a filename and give you your expected output:

sub domkfile {
    my ($fname, @flist)=shift;
    open my $fh, '<', $fname or die "Can't open `$fname': $!\n";
    push @flist, /SOURCE=\.\\(.*)$/i while <$fh>;
    "@flist";
}
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If slurping the whole file at once is not a problem, and indeed it should not be in this case, you may avoid the use of the @flist array with a map:

sub domkfile {
    my $fname=shift;
    open my $fh, '<', $fname or die "Can't open `$fname': $!\n";
    join ' ' => map /SOURCE=\.\\(.*)$/i, <$fh>;
}
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