Add copying code to the delivery action

use Cwd;

use Email::MIME;

use Email::Send;

use File::Copy;

use FindBin qw($RealBin $RealScript);

use Fcntl qw(:flock);

use IPC::Open3;

		email_delivery_manual("$project_path/$project", $email);

		return 1;

	}

	my $homedir = shift @homedirs;

	# Now, let's get to work

	# Start by getting the user's UID and GID.

	log_msg("Will do delivery to user $username\n");

	my @homedir_stat = stat($homedir);

	my $homedir_mode = $homedir_stat[3] & 07777;

	my $homedir_uid = $homedir_stat[4];

	my $homedir_gid = $homedir_stat[5];

	# Figure out what to call the folder name

	# We prefer to use the runfolder name, but if that exists already, then

	# fall back to some suffix like .0, .1, etc.

	my $runfolder_name = $runfolder;

	$runfolder_name =~ s{\A.+/(.+)\z}{$1}xims;

	my $i = -1;

	my $runfolder_suffix = '';

	while (-r "$homedir/$runfolder_name$runfolder_suffix") {

		if ($runfolder_suffix eq '') {

			$runfolder_suffix = '.0';

		} else {

			$i++;

			$runfolder_suffix = ".$i";

		}

	}

	my $destination = "$homedir/$runfolder_name$runfolder_suffix";

	log_msg("Will deliver files to $destination");

	# Create the directory to hold everything

	mkdir($destination, $homedir_mode);

	chown($homedir_uid, $homedir_gid, $destination);

	# Now let's begin to deliver everything

	deliver_directory("$project_path/$project", $destination,

	                  $homedir_uid, $homedir_gid);

	# All done!

	return 1;

}

# deliver_directory: Copy a directory to the destination, and chown

sub deliver_directory {

	my ($source, $destination, $uid, $gid) = @_;

	# Start listing the source directory contents

	my $source_handle;

	opendir($source_handle, $source) or do {

		log_msg(<<"EOF");

We were unable to read the source directory for our copy.

The directory we tried to read is: $source

The error we got is: $!

EOF

		return 0;

	};

	# Copy everything we find (but not . or ..)

	while (my $item = readdir($source_handle)) {

		next if $item eq '.';

		next if $item eq '..';

		# Work out the file/directory target and mode

		my $target = "$destination/$item";

		my $mode = (stat("$source/$item"))[2] & 07777;

		log_msg("$source/$item -> $target, mode $mode\n");

		# Files are easy enough to copy

		if (-f "$source/$item") {

			File::Copy::copy("$source/$item", $target) or do {

				log_msg(<<"EOF");

We were unable to copy $item to its destination, because of an error.

The file we tried to copy is: $source/$item

The destination was: $target

The error is: $!

EOF

				return 0;

			};

			chmod($mode, $target);

			chown($uid, $gid, $target);

		}

		# For directories, we make the directory and then recurse

		elsif (-d "$source/$item") {

			mkdir($target, $mode);

			chown($uid, $gid, $target);

			my $res = deliver_directory("$source/$item", $target);

			return $res unless $res == 1;

		}

		# Skip other stuff

		else {

			log_msg("Skipping $source/$item, which is neither a ");

			log_msg("file nor a directory.\n");

		}

	}

	# All done with this directory!

	closedir($source_handle);

	return 1;

}

# Given a runfolder, return the path to the laneBarcode.html file

sub barcode_path {

	my ($runfolder) = @_;