They shouldn't be in the repo

target/classes/plugins/ylemontag/matlabcommunicator/icy_command.m

-
-function args_out = icy_command(class_name, command, args_in)%#ok
-% args_out = icy_command(class_name, command, args_in)
-% 
-% Low-level function to execute a command in Icy from Matlab.
-%
-% This function should not be used directly by final-users.
-
-% Sessions identifiers
-mlock;
-persistent client_ID;
-persistent path_in  ;
-persistent path_out ;
-
-% Loop for session ID renewing
-remaining_attemps = 2;
-while(true)
-
-	% Get a session ID if necessary
-	if(~exist('client_ID', 'var') || isempty(client_ID))
-		msg_in    = cell(1, 1);
-		msg_in{1} = '?';
-		msg_out   = send_command(msg_in);
-		if(length(msg_out)~=4 || ~strcmp(msg_out{1}, 'ID'))
-			error('Unconsistent answer (expected: ID)');
-		end
-		client_ID = msg_out{2};
-		path_in   = msg_out{3};
-		path_out  = msg_out{4};
-	end
-	remaining_attemps = remaining_attemps - 1;
-
-	% Write the in file
-	if(~exist('args_in', 'var'))
-		args_in = struct();%#ok
-	end
-	save(path_in, '-struct', 'args_in');
-	
-	% Execute the command
-	msg_in    = cell(3, 1);
-	msg_in{1} = client_ID;
-	msg_in{2} = class_name;
-	msg_in{3} = command;
-	msg_out   = send_command(msg_in);
-
-	% Interpret the result
-	if(length(msg_out)<1)
-		error('Unconsistent answer (no return code)');
-	end
-
-	% Code=='OK' => everything went well
-	if(strcmp(msg_out{1}, 'OK'))
-		args_out = load(path_out);
-		return;
-
-	% Code=='Fail' => error while executing the command
-	elseif(strcmp(msg_out{1}, 'Fail'))
-		error_message = '';
-		for p = 2:length(msg_out)
-			error_message = sprintf('%s\n  %s', error_message, msg_out{p});
-		end
-		error('Error while executing the command "%s" with the plugin %s:%s', ...
-			command, class_name, error_message);
-
-	% Code=='Bad ID' => try to renew the client ID once
-	elseif(strcmp(msg_out{1}, 'Bad ID'))
-		if(remaining_attemps>0)
-			client_ID = [];
-			path_in   = [];
-			path_out  = [];
-		else
-			error('Invalid client ID: %s', client_ID);
-		end
-
-	% Code=='Bad class name' => the expected plugin interpreter does not exist on Icy
-	elseif(strcmp(msg_out{1}, 'Bad class name'))
-		error('The expected plugin (%s) is not installed on Icy', class_name);
-
-	% Unkown return code
-	else
-		error('Unconsistent answer (unknown return code: %s)', msg_out{1});
-	end
-end
-
-% Core function
-function msg_out = send_command(msg_in)
-	
-	% Java stuff
-	import java.net.Socket
-	import java.io.*
-
-	% Establish the connection
-	socket = Socket('localhost', 8732);
-	out = socket.getOutputStream;
-	in  = socket.getInputStream ;
-
-	% Send the list of strings
-	for k=1:length(msg_in)
-		buffer_in = uint8(sprintf('%s\n', msg_in{k}));
-		%fprintf('In: %s', buffer_in);
-		out.write(buffer_in);
-	end
-	out.flush();
-
-	% Wait for the answer and close the connection
-	msg_out    = cell(0, 1);
-	msg_idx    = 0;
-	buffer_out = zeros(1, 256);
-	buffer_idx = 0;
-	while(true)
-		current_char = in.read();
-		if(current_char<0)
-			error('End of stream reached unexpectedly');
-		elseif(current_char==10 || current_char==13)
-			current_answer = char(buffer_out(1:buffer_idx));
-			%fprintf('Out: %s\n', current_answer);
-			if(strcmp(current_answer, 'EOF'))
-				break;
-			end
-			msg_idx = msg_idx + 1;
-			msg_out{msg_idx} = current_answer;
-			buffer_out = zeros(1, 256);
-			buffer_idx = 0;
-		else
-			buffer_idx = buffer_idx + 1;
-			buffer_out(buffer_idx) = current_char;
-		end
-	end
-	socket.close();
-end
-
-end

target/classes/plugins/ylemontag/matlabcommunicator/icy_init.m

-
-function icy_init()
-% icy_init()
-%
-% Append to the PATH Matlab environment variable all the folders that contain
-% Matlab functions in the Icy plugin directory.
-%
-% To initialize the functions provided by the Matlab<->Icy interaction plugins,
-% you have to execute the following commands each time you start Matlab:
-% 
-% >> addpath('path/to/icy/plugins/ylemontag/matlabcommunicator');
-% >> icy_init();
-%
-% This operation can be done automatically using a startup.m file (please
-% consult the Matlab documentation for more details).
-
-% Current path
-myself = mfilename('fullpath');
-
-% Text file containing the list of source folders
-sep = find(myself=='/', 1, 'last');
-communicator_root  = myself(1:sep);
-source_folder_file = [communicator_root 'source_folders.txt'];
-
-% Exit now if the source file does not exist
-if(~exist(source_folder_file, 'file'))
-	return;
-end
-
-% Read the file
-fid  = fopen(source_folder_file, 'r');
-line = fgetl(fid);
-while(ischar(line))
-	if(exist(line, 'dir'))
-		addpath(line);
-	end
-	line = fgetl(fid);
-end
-fclose(fid);

target/maven-archiver/pom.properties

-artifactId=matlab-communicator
-groupId=org.bioimageanalysis.icy
-version=1.0.5

target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst

-plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon$1.class
-plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon.class
-plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon$2.class
-plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer$2.class
-plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer$1.class
-plugins/ylemontag/matlabcommunicator/MatlabSession.class
-plugins/ylemontag/matlabcommunicator/MatlabCommandException.class
-plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer$MatlabSocket.class
-plugins/ylemontag/matlabcommunicator/MatlabInterpreter.class
-plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer.class

target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst

-/run/media/kitwaii/Dev/kitwaii/pasteur/Plugins/matlab-communicator/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorServer.java
-/run/media/kitwaii/Dev/kitwaii/pasteur/Plugins/matlab-communicator/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabCommandException.java
-/run/media/kitwaii/Dev/kitwaii/pasteur/Plugins/matlab-communicator/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabSession.java
-/run/media/kitwaii/Dev/kitwaii/pasteur/Plugins/matlab-communicator/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabInterpreter.java
-/run/media/kitwaii/Dev/kitwaii/pasteur/Plugins/matlab-communicator/src/main/java/plugins/ylemontag/matlabcommunicator/MatlabCommunicatorDeamon.java