I think the consensus is clearly that $_ has a newline on it, but just wanted to add one other note -- system() can take the program and argument list as well:

chomp;
my @args = ("$user\@$ip:$source/$_", "staging/$_");
my $command = "scp";
system $command, @args;
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This still requires the chomp, but might make the code more legible or easier to debug and I believe (but not sure) that in some cases it helps with escaping issues.