diff --git a/.gitignore b/.gitignore
index b0afd4835bf581456c0cf7f6dc7bcd8139cddf34..3d5fc69ca1e50965038a6e833ed09a2d1a9d32a8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -26,7 +26,13 @@ codegen/
 
 # Personal test files
 test*.m
+test123_data.h5
+
+# files that are created in example.m
+testdata_2.h5
+test_data.mat
 export/*
 
 # Octave session info
 octave-workspace
+test_data.mat 
diff --git a/CI_files/default_test.m b/CI_files/default_test.m
new file mode 100644
index 0000000000000000000000000000000000000000..515ad3718e2c3c0b06b6e037da2f6343796055eb
--- /dev/null
+++ b/CI_files/default_test.m
@@ -0,0 +1,66 @@
+function [result] = default_test()
+%UNTITLED2 This is a simple test if Plot ID works for the default settings
+%   Detailed explanation goes here
+
+clear; clc; close all;
+addpath('./fcn_core','./fcn_help');
+
+ProjectID = 'Test01';
+%% Data
+% some random data
+x = linspace(0,7);
+y = rand(1,100)+2;
+dataset1 = 'test_data.mat';
+save('CI_files/test_data.mat','x','y');
+% some data as .h5
+x1 = linspace(0,2*pi);
+y1 = sin(x1)+2;
+
+% define file path & name
+fpath = "CI_files/testdata_2.h5";
+dataset2 = 'testdata_2.h5';
+
+% create hdf5 file and dataset > write data to hdf5 file / dataset
+h5create(fpath, "/x1", size(x1), "Datatype", class(x1))
+h5create(fpath, "/y1", size(y1), "Datatype", class(y1))
+h5write(fpath, "/x1", x1)
+h5write(fpath, "/y1", y1)
+
+%% Plotting
+
+fig(1) =figure('visible','off');
+plot(x,y,'-k');
+hold on
+plot(x1,y1,'-r');
+
+%% Tag the plot
+try
+    [figs, ID] = TagPlot(fig, ProjectID);
+
+    %% call a dummy function
+    a=1;
+    a = example_fcn(a);
+
+    %% publishing
+
+    % The functions needs the file location, the location of the data and the
+    % figure
+    path.script = mfilename('fullpath'); % filename of the m.script
+
+    % file name of the data
+    path.rdata =  {dataset1,dataset2} ; % don't forget the extension
+
+    Publish(path, ID, figs, 'Location', 'CI-Test')
+    
+    % clean up 
+    delete CI_files/export/* CI_files/*.mat CI_files/*.h5 
+    rmdir('CI_files/export','s'); 
+    result = true;
+    clc;
+catch
+    result = false;
+    warning('simple_test failed');
+end
+
+end
+
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000000000000000000000000000000000000..a612ad9813b006ce81d1ee438dd784da99a54007
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,373 @@
+Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+    means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+    means
+
+    (a) that the initial Contributor has attached the notice described
+        in Exhibit B to the Covered Software; or
+
+    (b) that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the
+        terms of a Secondary License.
+
+1.6. "Executable Form"
+    means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+    means a work that combines Covered Software with other material, in
+    a separate file or files, that is not Covered Software.
+
+1.8. "License"
+    means this document.
+
+1.9. "Licensable"
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+1.10. "Modifications"
+    means any of the following:
+
+    (a) any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered
+        Software; or
+
+    (b) any new file in Source Code Form that contains any Covered
+        Software.
+
+1.11. "Patent Claims" of a Contributor
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+1.12. "Secondary License"
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+1.13. "Source Code Form"
+    means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, "You" includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, "control" means (a) the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or (b) ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+    or
+
+(b) for infringements caused by: (i) Your and any other third party's
+    modifications of Covered Software, or (ii) the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+*                                                                      *
+*  6. Disclaimer of Warranty                                           *
+*  -------------------------                                           *
+*                                                                      *
+*  Covered Software is provided under this License on an "as is"       *
+*  basis, without warranty of any kind, either expressed, implied, or  *
+*  statutory, including, without limitation, warranties that the       *
+*  Covered Software is free of defects, merchantable, fit for a        *
+*  particular purpose or non-infringing. The entire risk as to the     *
+*  quality and performance of the Covered Software is with You.        *
+*  Should any Covered Software prove defective in any respect, You     *
+*  (not any Contributor) assume the cost of any necessary servicing,   *
+*  repair, or correction. This disclaimer of warranty constitutes an   *
+*  essential part of this License. No use of any Covered Software is   *
+*  authorized under this License except under this disclaimer.         *
+*                                                                      *
+************************************************************************
+
+************************************************************************
+*                                                                      *
+*  7. Limitation of Liability                                          *
+*  --------------------------                                          *
+*                                                                      *
+*  Under no circumstances and under no legal theory, whether tort      *
+*  (including negligence), contract, or otherwise, shall any           *
+*  Contributor, or anyone who distributes Covered Software as          *
+*  permitted above, be liable to You for any direct, indirect,         *
+*  special, incidental, or consequential damages of any character      *
+*  including, without limitation, damages for lost profits, loss of    *
+*  goodwill, work stoppage, computer failure or malfunction, or any    *
+*  and all other commercial damages or losses, even if such party      *
+*  shall have been informed of the possibility of such damages. This   *
+*  limitation of liability shall not apply to liability for death or   *
+*  personal injury resulting from such party's negligence to the       *
+*  extent applicable law prohibits such limitation. Some               *
+*  jurisdictions do not allow the exclusion or limitation of           *
+*  incidental or consequential damages, so this exclusion and          *
+*  limitation may not apply to You.                                    *
+*                                                                      *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+  This Source Code Form is subject to the terms of the Mozilla Public
+  License, v. 2.0. If a copy of the MPL was not distributed with this
+  file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+  This Source Code Form is "Incompatible With Secondary Licenses", as
+  defined by the Mozilla Public License, v. 2.0.
diff --git a/copiedFile.h5 b/copiedFile.h5
deleted file mode 100644
index 4ddca81c276e204d2476b044f5a2fda057105080..0000000000000000000000000000000000000000
Binary files a/copiedFile.h5 and /dev/null differ
diff --git a/example.m b/example.m
index e25950de4b3bf0e7bb0edb41c76791a8d3992e30..f208097f48304f8ca96fbc5dd1907c184233b44a 100644
--- a/example.m
+++ b/example.m
@@ -1,14 +1,28 @@
-% test skript
+%% Example Script
+% This Script is meant to demonstrate the capabilities of the PlotID tool.
+
+%% Clear Environment
 clear; clc; close all;
 addpath('fcn_core','fcn_help');
+addpath('CI_files'); % Test scripts
 
 try
     delete testdata_2.h5;
 end
 
+
+%% Set ProjectID
+% ProjectID 
+
+% TODO:  decide how projectID and optionally ORCID will be implemented
+% ORCID placed on startup (alternative?) - projectID as persistent
+% otherwise dialogue?
 ProjectID = 'JL01';
+
+
+
 %% Data
-% some random data
+% Creating Random Data to use as data-file
 
 x = linspace(0,7);
 y = rand(1,100)+2;
@@ -30,30 +44,52 @@ h5create(fpath, "/y1", size(y1), "Datatype", class(y1))
 h5write(fpath, "/x1", x1)
 h5write(fpath, "/y1", y1)
 
-%% Plotting
 
-fig(1) =figure;
+%% Plotting
+% This is still part of a normal script to produce plots.
+% Make sure to save each figure in a variable to pass to PlotID-functions.
+fig(1) = figure;
 plot(x,y,'-k');
 box off
 set(gca, 'TickDir', 'out', 'YLim', [0,4]);
 
 hold on
-%fig(2) =figure;
+%fig(2) = figure;
 plot(x1,y1,'-r');
 set(gca, 'TickDir', 'out', 'YLim', [0,4]);
 
-% Tag the plot
+%% Tag the plot
+% PlotID Implementation starts here.
+ 
 [figs, ID] = TagPlot(fig, ProjectID);
 
-%% publishing
 
+
+%% call a dummy function
+% Place for post-processing of the plot, or additional related code.
+a=1;
+a = example_fcn(a);
+
+%% Publishing
+% Second part of plotID 
 % The functions needs the file location, the location of the data and the
-% figure
-path.script = mfilename('fullpath') % filename of the m.script
+% figure and can take several options.
+% TODO add explanations for Options
+path.script = mfilename('fullpath'); % filename of the m.script
 
-% file name of the data (should be extended to handle arrays)
+% file name of the dataset
 path.rdata =  {dataset1,dataset2} ; % don't forget the extension
 
+Publish(path, ID, figs, 'Location', 'local','Method','centraliced')
+
+%% Second Plot with identical data to test centralized method
+% 
+
+fig2 =figure;
+plot(x,y,'-k');
+hold on
+plot(x1,y1,'-r');
 
-Publish(path, ID, figs, 'Location', 'local','Method','individual')
+[fig2, ID] = TagPlot(fig2, ProjectID);
 
+Publish(path, ID, fig2, 'Location', 'local','Method','centraliced')
\ No newline at end of file
diff --git a/example_fcn.m b/example_fcn.m
new file mode 100644
index 0000000000000000000000000000000000000000..418f15ca734ac8423bdda5a6ead2c32af6820e22
--- /dev/null
+++ b/example_fcn.m
@@ -0,0 +1,6 @@
+function [outputArg1] = example_fcn(inputArg1)
+%TEST_2 just a dummy function
+outputArg1 = inputArg1;
+
+end
+
diff --git a/fcn_core/CreateID.m b/fcn_core/CreateID.m
index 94d0df2216f9732540f21ae68b7eaccc9c8a2c8a..42ec2b29e9c2c041ecbe190175d07cf219deef02 100644
--- a/fcn_core/CreateID.m
+++ b/fcn_core/CreateID.m
@@ -11,7 +11,12 @@ switch method
         ID = posixtime(datetime('now')); %get current Unix time
         ID = dec2hex(int32(ID)); % get it as Hex
         pause(0.5); %Pausing for unique IDs
-    otherwise
+    case 2 % random UUID from Java 128 bit
+        %Static factory to retrieve a type 4 (pseudo randomly generated) UUID.
+        % The UUID is generated using a cryptographically strong pseudo random number generator.
+        temp =  java.util.UUID.randomUUID;
+        ID = temp.toString;           
+     otherwise
         error('The requested method is not defined yet');
 end
 
diff --git a/fcn_core/Publish.m b/fcn_core/Publish.m
index eb0c428aebddba8a2311df6acb31d39c4af097ce..e6952d70589138df8eec1b9e2f3b7f74f5a3f1e2 100644
--- a/fcn_core/Publish.m
+++ b/fcn_core/Publish.m
@@ -11,15 +11,18 @@ arguments
    DataPaths
    ID (1,:) {mustBeNonzeroLengthText} % ID must be provided
    figures (1,:) {mustBeFigure} % Checks if Figures are figures
-   options.Location {mustBeMember(options.Location ,['local','server'])} = 'local' % storage path
+   options.Location {mustBeMember(options.Location ,['local','server','CI-Test'])} = 'local' % storage path
    options.Method {mustBeMember(options.Method ,['individual','centraliced'])} = 'individual'
+   options.CopyUserFCN (1,1) {mustBeNumericOrLogical} = true 
 end
 
 switch options.Location 
     case 'local'
          storPath = fullfile(pwd,'export');
     case 'server'
-        storPath = '\\FST-220\Jans-50GB-SMB\Lemmer'; 
+        storPath = '\\FST-220\Jans-50GB-SMB\Lemmer';
+    case 'CI-Test'
+        storPath = fullfile(pwd,'CI_files','export');
 end
 folderName = char(ID);
 
@@ -32,40 +35,52 @@ end
 
 disp('Publishing started');
 
-%% Create a Copy of the script
+%% Create a Copy of the script and User functions(optional)
+createFileCopy({[DataPaths.script,'.m']},folderName,storPath,ID, 'script');
 
-try
-    %FileNameAndLocation=['C:\Users\Lemmer\Documents\GitLab\plot_identifier\MATLAB\test'];
-    FileNameAndLocation= DataPaths.script;
-    newbackup=sprintf([ID,'_script.m']);
-    currentfile=strcat(FileNameAndLocation, '.m');
-    % Write a Copy of the Plotting Script 
-    RemotePath = fullfile(storPath,folderName, newbackup);
-    copyfile(currentfile,RemotePath);
-    disp('Script sucessfully published');
-catch
-   warning('Script export was not sucessful')
+if options.CopyUserFCN
+   [fList,pList] = matlab.codetools.requiredFilesAndProducts(DataPaths.script);
+   % plist contains the required MATLAB Toolboxes, maybe usefull in future
+   fList = fList(~ismember(fList,[DataPaths.script,'.m'])); % rmv script from list
+   fList = removePltIdFiles(fList); % Do not copy files that are part of plot ID
+   if ~isempty(fList)
+       createFileCopy(fList,folderName,storPath,ID,'userFcn');
+   end
 end
+
 %% Research data handeling
 switch options.Method
     case 'centraliced' % Work in progresss!!!
-        %check if data folder exists
+        % check if data folder exists
         if ~isfolder(fullfile(storPath,'data'))
             mkdir(fullfile(storPath,'data'));
         end
+        %list all files
+        fList = dir(fullfile(storPath,'data', '**\*.*'));  %get list of files and folders in any subfolder
+        fList = fList(~[fList.isdir]);  %remove folders from list
+        fList = struct2table(fList);
+        
         % Check if the new plot is based on the original data-set    
             % copy the data(once)
-            createFileCopy(DataPaths.rdata,'data',storPath,ID);
-        % create a linked (soft) copy
-            
-        
-               
+        for i=1:numel(DataPaths.rdata)            
+            % check if identical file exists (status = 1)
+            [~, idx] = fileCompare(DataPaths.rdata{i},fList);
+            % create Linked HDF5 files for identical files
+            if any(idx)
+            sourcePath = fList.name{idx}; % If there are multiple copies already, this only picks the last entry
+            if contains(sourcePath,{'.h5','.hdf5'}) % Linking only for HDF5
+                createLinkedHDF5(sourcePath,storPath,ID);
+            end
+            else % no identical file exists
+               createFileCopy(DataPaths.rdata{i},'data',storPath,ID,'dataCentral');
+            end
+        end
     case 'individual'
         % Create a copy of the research data    
-        createFileCopy(DataPaths.rdata,folderName,storPath,ID);
+        createFileCopy(DataPaths.rdata,folderName,storPath,ID, 'data');
 end
 %% Export the Plots
-%try 
+try 
    for i=1:numel(figures)
        fig = figures(i);
        PlotName = [ID,'_plot',num2str(i)]; % Der Plotnamen
@@ -75,34 +90,14 @@ end
        exportgraphics(fig,[RemotePath,'.png'],'Resolution',300);
        disp([num2str(i),' of ',num2str(numel(figures)),' figures exported']);
    end
-%catch 
-    %warning('Plot export was not sucessful')
-%end
+catch 
+    warning('Plot export was not successful')
+end
 
-disp(['Publishing of ', ID , ' done']);
+disp(['publishing of ', ID , ' done']);
 
 end %function
 
-function [] = createFileCopy(filePaths,folderName,storPath,ID)
-% Creates a copy of the files (can used for multiple paths in a cell array)
-% folderName is the name of the exporting folder
-    disp('Start to copy research data ...');   
-    try        
-        for i = 1:numel(filePaths)
-            FileNameAndLocation = filePaths{i};
-            [~,~,ext] = fileparts(filePaths{i}); % get the extension
-            newbackup = sprintf([ID,'_data',ext]);
-
-            % Write the copied file
-            RemotePath = fullfile(storPath,folderName, newbackup);
-            copyfile(FileNameAndLocation,RemotePath);
-        end
-        disp('Research data sucessfully published');
-    catch
-        warning('Research data export was not sucessful')
-    end %try
-end
-
 function tf = mustBeFigure(h)
 %checks if input is a figure object
   tf = strcmp(get(h, 'type'), 'figure') & isa(h, 'matlab.ui.Figure');
diff --git a/fcn_core/TagPlot.m b/fcn_core/TagPlot.m
index 3c426266624a4a9dd64e93d970428c2fe08837a0..4fac128393edd75b1b7877cee7ce29eb517f54c1 100644
--- a/fcn_core/TagPlot.m
+++ b/fcn_core/TagPlot.m
@@ -1,16 +1,50 @@
-function [figs, ID] = TagPlot(figs, prefix)
+function [figs, ID] = TagPlot(figs, prefix, options)
 %TagPlot adds IDs to figures
 %   The ID is placed visual on the figure window and as Tag (Property of figure)
 %   TagPlot can tag multiple figures at once
+%   prefix is the project number (string or char)
+%   
+%   The ID is placed on the 'east' per default, if you want it somwhere
+%   else, use the 'Location' option. 'north','east','south','west' are
+%   predefined, otherwise use the 'custom' option and provide the desired
+%   'Position' (relative to your x- and y-axis limits)
 arguments
     figs (1,:) {mustBeFigure}
     prefix (1,:) {mustBeText}= ''
+    options.Fontsize (1,1) {mustBeInteger} = 8 
+    options.Location (1,:) {mustBeText} = 'east'
+    options.Position (1,2) {mustBeVector} = [1,0.4] % default for east
+    options.Rotation (1,1) {mustBeInteger} = 0  
 end
 
 if isempty(prefix)
     warning('no project prefix defined')
 end
 
+switch options.Location
+    case 'north'
+        options.Position = [0.4,0.95];
+        options.Rotation = 0;
+    case 'east'
+        options.Position = [1,0.4];
+        options.Rotation = 90;
+    case 'south'
+        options.Position = [0.4,.02];
+        options.Rotation = 0;
+    case 'west'
+        options.Position = [.05,0.4];
+        options.Rotation = 90;
+    case 'custom'
+        % Check if Position is valid
+        if ~all(0 <= options.Position & options.Position <= 1)
+           options.Position = [1,0.4];
+           warning('options.Position is not valid, TagPlot default values instead');
+        end
+    otherwise % set default position
+        warning([options.Location, ' is not a defined location, TagPlot uses location east instead']);
+        options.Location = 'east'; options.Position = [1,0.4];
+end
+    
 for n = 1:numel(figs)
     ID = CreateID; % Create ID
     ID = [prefix,'-',ID]; % add Prefix
@@ -19,8 +53,10 @@ for n = 1:numel(figs)
     ylim =get(axes,'YLim');
     xlim =get(axes,'XLim');
     %ID
-    text(axes,xlim(2),0.4*ylim(2), ID,'Fontsize',8,'Rotation',90,'VerticalAlignment','bottom',...
-    'Color', 0.65*[1 1 1],'BackgroundColor','w');
+    position = [options.Position(1)*xlim(2), options.Position(2)*ylim(2)];
+    text(axes,position(1),position(2), ID,'Fontsize',options.Fontsize,...
+    'Rotation',options.Rotation, 'VerticalAlignment','bottom','Color',...
+        0.65*[1 1 1],'BackgroundColor','w');
     set(figs(n),'Tag', ID);
     
 end
diff --git a/fcn_help/FileCompare.m b/fcn_help/FileCompare.m
deleted file mode 100644
index aa5adfe3cbce82b1627760697908143b11894e53..0000000000000000000000000000000000000000
--- a/fcn_help/FileCompare.m
+++ /dev/null
@@ -1,29 +0,0 @@
-function [status] = fileCompare(filename1,filename2)
-%UNTITLED2 Summary of this function goes here
-%   Detailed explanation goes here
-
-[~,~,ext1] = fileparts(filename1); 
-[~,~,ext2] = fileparts(filename2);
-
-if ~isequal(ext1,ext2)
-    warning('File extension are not identical');
-    status = false;
-    return
-end
-
-if ispc
-    filename2 = 'export\JL01-60DB3572\JL01-60DB3572_data.h5';
-    filename1 = 'export\JL01-60DB3576\JL01-60DB3576_data.h5';
-    [status,result] = system(['fc ' filename1 ' ' filename2]);
-
-elseif isunix %untested!
-    filename2 = 'export/JL01-60DB3572/JL01-60DB3572_data.h5';
-    filename1 = 'export/JL01-60DB3576/JL01-60DB3576_data.h5';
-    [status,result] = system(['diff ' filename1 ' ' filename2]);
-else
-    warning('Platform not supported')
-end
-
-
-end
-
diff --git a/fcn_help/createFileCopy.m b/fcn_help/createFileCopy.m
new file mode 100644
index 0000000000000000000000000000000000000000..4bf198e429c269dbdc75f42e846f4e416b3a0130
--- /dev/null
+++ b/fcn_help/createFileCopy.m
@@ -0,0 +1,52 @@
+function [] = createFileCopy(filePaths,folderName,storPath,ID,type)
+% Creates a copy of the files (can be used for multiple paths in a cell array)
+% folderName is the name of the exporting folder
+    disp(['start to copy ', type]);  
+    
+    if ~iscell(filePaths)
+        %fixes Issue if Filepath is a char and not a cell array
+        filePaths = {filePaths};
+    end
+        
+    try        
+        for i = 1:numel(filePaths)
+            FileNameAndLocation = filePaths{i};
+            [~,name,ext] = fileparts(filePaths{i}); % get the extension
+                          
+            switch type
+                case 'data'
+                    sufix = '_data';
+                    newfile = sprintf([ID, sufix, '_' , num2str(i) ,ext]);
+                case 'dataCentral'
+                    %keep original name
+                    newfile = sprintf([name,ext]);
+                case 'script'
+                    sufix = '_script';
+                    newfile = sprintf([ID, sufix ,ext]);
+                case 'userFcn'
+                    %keep original name
+                    newfile = sprintf([name,ext]);
+                otherwise 
+                    error([type,' is not a valid type for createFileCopy'])
+            end %switch 
+            
+            % Write the file
+            RemotePath = fullfile(storPath,folderName, newfile);
+            
+%           Check if remote file already exists
+            count = 0;
+            while isfile(RemotePath) && ismember(type,{'data','dataCentral'})
+                % Add a Sufix number to new file name
+                count = count + 1;
+                [~,name,ext] = fileparts(RemotePath);
+                RemotePath = fullfile(storPath,folderName,...
+                    [name,'_',num2str(count),ext]);
+            end
+            copyfile(FileNameAndLocation,RemotePath);
+        end
+        disp([type, ' sucessfully published']);
+    catch
+        warning([type,' export was not sucessful'])
+   end %try
+end
+
diff --git a/fcn_help/createLinkedHDF5.m b/fcn_help/createLinkedHDF5.m
index 5b1e9716ccd5219e8756ae0af60b23c0d6ac282c..2738fd173b7e00ed36cadad45912c79246c6a872 100644
--- a/fcn_help/createLinkedHDF5.m
+++ b/fcn_help/createLinkedHDF5.m
@@ -1,20 +1,20 @@
 function [status] = createLinkedHDF5(SourceFile,TargetPath,ID)
-%UNTITLED4 Summary of this function goes here
-%   Detailed explanation goes here
+%createLinkedHDF5 creates a HDF file that references the Sourcefile
+%   TargetPath is the storage location, ID the foldername
+%   Status returns true if the function was sucessfull
 
 plist_id = 'H5P_DEFAULT';
 
-% Work in Progress... Problem mit dem Pfad...
-
-try
-    fid = H5F.create(fullfile(TargetPath,[ID,'_data.h5']));
+% try
+    fid = H5F.create(fullfile(TargetPath,ID,[ID,'_data.h5']));
     %create External Link to Sourcefile in the Group linkToExternal
-    H5L.create_external(SourceFile,'/',fid,'linkToExternal',plist_id,plist_id);
+    H5L.create_external(['..\data\',SourceFile],'/',fid, SourceFile ,plist_id,plist_id);
     H5F.close(fid);
     status = 1;
-catch
-    warning('No linked HDF file was created');
-    status = 0;
-end
+% catch
+%     warning('No linked HDF file was created');
+%     status = 0;
+% end
+
 end
 
diff --git a/fcn_help/fileCompare.m b/fcn_help/fileCompare.m
new file mode 100644
index 0000000000000000000000000000000000000000..c9007e704eb7a8ff8870830bc2d6610dce185107
--- /dev/null
+++ b/fcn_help/fileCompare.m
@@ -0,0 +1,49 @@
+function [status, id] = fileCompare(filename,fileList)
+%fileCompare checks if file1 is (binary) identical to a file in filelist
+% it returns a sttus and the id of the identical file
+% the functions uses the windows system function fc or the unix function
+% diff
+
+if isempty(fileList)
+   % no comparison necessary
+    status =false;
+    id = 0;
+    return
+end
+
+[~,~,ext1] = fileparts(filename); 
+id = zeros(height(fileList),1);
+
+for i=1:height(fileList)
+    [~,~,ext2] = fileparts(fileList.name{i});
+
+    if ~isequal(ext1,ext2)
+        %warning('File extension are not identical');
+        status = false;
+        continue
+    end
+
+    filepath = fullfile(fileList.folder{i},fileList.name{i});
+    if ispc
+        [status,~] = system(['fc ' filename ' ' filepath]);
+        % 0 -> identical, 1 -> not identical
+         status = ~status; % false (not identical), true(identical)
+                   
+    elseif isunix %untested!
+        [status,~] = system(['diff ' filename ' ' filepath]);
+    else
+        warning('Platform not supported')
+    end
+    
+    if status == 1        
+        id(i) = 1;
+    else 
+        % Status can also be any other number e.g. 2 
+        id(i) = 0;
+    end
+    
+    id =logical(id); %bugfix
+end
+
+end
+
diff --git a/fcn_help/removePltIdFiles.m b/fcn_help/removePltIdFiles.m
new file mode 100644
index 0000000000000000000000000000000000000000..3080c22985474f8d2227e2bd62c17ecbd6f3163f
--- /dev/null
+++ b/fcn_help/removePltIdFiles.m
@@ -0,0 +1,19 @@
+function [fListClean] = removePltIdFiles(fList)
+%removePltIdFiles removes functions that are part of PlotID out of flist
+%   Detailed explanation goes here
+%addpath('..\fcn_core');
+
+[~,names,ext] = fileparts(fList);
+names = strcat(names, ext); % add ext for comparison
+
+% Get a list of all .m files that are part of Plot id
+PltID_flist = struct2table([dir('fcn_help'); dir('fcn_core')]); %get list of files 
+[~,~,PltID_flist.ext(:)] = fileparts(PltID_flist.name(:)); % add ext column
+
+PltID_flist = PltID_flist(strcmp(PltID_flist.ext,'.m'),:);
+
+% Comparison and filter
+fListClean = fList(~ismember(names,PltID_flist.name));
+
+end
+
diff --git a/fcn_help/replaceLinkedHDF5.m b/fcn_help/replaceLinkedHDF5.m
new file mode 100644
index 0000000000000000000000000000000000000000..e84e49f6e3aeed36d24f59b50288984fbe4d3998
--- /dev/null
+++ b/fcn_help/replaceLinkedHDF5.m
@@ -0,0 +1,61 @@
+function replaceLinkedHDF5(linkedFilepath)
+% replaceLinkedHDF5 replaces the HDF5, that contains only a link to another
+% HDF5 File with a file containing the actual Data, thus turning it into an
+% independent data file. It essentially turns the plotID option
+% 'centralized' into 'individual'.
+%   Filepath is the location of the File that contains the link. The
+%   filepath to the linked data has to be present in the file itself.
+
+
+
+%% Check whether the only Objects present are links
+h5inf = h5info(linkedFilepath);
+
+% default behaviour dont overwrite
+overwrite = false;
+
+if isempty([h5inf.Groups, h5inf.Datasets, h5inf.Datatypes, h5inf.Attributes]) && ...
+      all(size(h5inf.Links) == [1 1])  
+    % There are no other known objects present and
+    % there is only one linked file
+       overwrite = true;
+end
+
+%% Create Copies of files
+for i = 1:size(h5inf.Links, 2)
+    % This is the file with full data  
+    linkTargetPath = h5inf.Links(i).Value{1,1}; 
+    % This is the empty file
+    % TODO filename decision
+    linkSourcePath = strcat(linkedFilepath,'_',num2str(i)); 
+
+    % Create an absolute path from the relative linking path
+    absoluteTP = regexp(linkSourcePath, filesep, 'split');
+    TargetPathSplit = regexp(linkTargetPath, filesep, 'split');
+    % How many levels do we need to go up in the relative path
+    % This is merely counting the occurances of '..' within the path, but
+    % should not cause issues if the realtive path was created by the
+    % linking process
+    levelsUp = sum(contains(TargetPathSplit,'..'));
+    absoluteTP = absoluteTP(1:(end-(1+levelsUp)) ); %Remove filename + levels
+    linkTargetPath = strjoin([absoluteTP, TargetPathSplit(~contains(TargetPathSplit,'..'))],filesep);
+    
+    if ~isfile(linkTargetPath)
+        warning(strcat("Link destination """,linkTargetPath,""" does not exist or relative path does not fit, no copy created"))
+    end
+    
+    if overwrite % can only be for i=1, and size = 1
+    linkSourcePath = linkedFilepath;
+    end
+    disp('Copying file from ', linkSourcePath, ' to ', linkTargetPath)
+    copyfile(linkTargetPath,linkSourcePath);
+    
+end
+        
+        
+    
+end
+
+
+
+
diff --git a/test_data.mat b/test_data.mat
deleted file mode 100644
index 06ca1639f8c3febb925fb5bbdc67b1953a894ab6..0000000000000000000000000000000000000000
Binary files a/test_data.mat and /dev/null differ
diff --git a/testdata_2.h5 b/testdata_2.h5
deleted file mode 100644
index efc071f84eaf0f39c147f2e74f80c4666ff22467..0000000000000000000000000000000000000000
Binary files a/testdata_2.h5 and /dev/null differ