2755: Merge branch '2755-require-keep-permission' refs #2755

diff --combined sdk/cli/bin/crunch-job
index 5da8c78dda143cfac7befabd9fd6ba2610f5d21a,e30efd902445fe46eebd467800248428213c45ef..8b4717734a0450f2f25d652eeb35589e4fa2ebc9
--- 1/sdk/cli/bin/crunch-job
--- 2/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@@ -641,8 -641,8 +641,8 @@@ for (my $todo_ptr = 0; $todo_ptr <= $#j
      $command .= "&& exec arv-mount --allow-other $ENV{TASK_KEEPMOUNT} --exec ";
      if ($docker_image)
      {
 -      $command .= "crunchstat -cgroup-parent=/sys/fs/cgroup/lxc -cgroup-cid=$ENV{TASK_WORK}/docker.cid -poll=1000 ";
 -      $command .= "$docker_bin run -i -a stdin -a stdout -a stderr -cidfile=$ENV{TASK_WORK}/docker.cid ";
 +      $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -cgroup-parent=docker -cgroup-cid=$ENV{TASK_WORK}/docker.cid -poll=10000 ";
 +      $command .= "$docker_bin run -i -a stdin -a stdout -a stderr --cidfile=$ENV{TASK_WORK}/docker.cid ";
        # Dynamically configure the container to use the host system as its
        # DNS server.  Get the host's global addresses from the ip command,
        # and turn them into docker --dns options using gawk.
@@@ -661,9 -661,8 +661,9 @@@
        }
        $command .= "\Q$docker_image\E ";
      } else {
 -      $command .= "crunchstat -cgroup-path=/sys/fs/cgroup "
 +      $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -poll=10000 "
      }
 +    $command .= "stdbuf -o0 -e0 ";
      $command .= "$ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
      my @execargs = ('bash', '-c', $command);
      srun (\@srunargs, \@execargs, undef, $build_script_to_send);
@@@ -821,20 -820,22 +821,22 @@@ if ($collated_output
          or die "failed to get collated manifest: $!";
      # Read the original manifest, and strip permission hints from it,
      # so we can put the result in a Collection.
-     my @manifest_lines = ();
+     my @stripped_manifest_lines = ();
+     my $orig_manifest_text = '';
      while (my $manifest_line = <$orig_manifest>) {
+       $orig_manifest_text .= $manifest_line;
        my @words = split(/ /, $manifest_line, -1);
        foreach my $ii (0..$#words) {
          if ($words[$ii] =~ /^[0-9a-f]{32}\+/) {
            $words[$ii] =~ s/\+A[0-9a-f]{40}@[0-9a-f]{8}\b//;
          }
        }
-       push(@manifest_lines, join(" ", @words));
+       push(@stripped_manifest_lines, join(" ", @words));
      }
-     my $manifest_text = join("", @manifest_lines);
+     my $stripped_manifest_text = join("", @stripped_manifest_lines);
      my $output = $arv->{'collections'}->{'create'}->execute('collection' => {
-       'uuid' => md5_hex($manifest_text),
-       'manifest_text' => $manifest_text,
+       'uuid' => md5_hex($stripped_manifest_text),
+       'manifest_text' => $orig_manifest_text,
      });
      $Job->update_attributes('output' => $output->{uuid});
      if ($Job->{'output_is_persistent'}) {