diff --git a/Build-Example.py b/Build-Example.py
new file mode 100644
index 0000000..69b64af
--- /dev/null
+++ b/Build-Example.py
@@ -0,0 +1,62 @@
+"""
+Python script to build a dissertaion based on Markdown / Pandoc
+
+TODO: Options?
+"""
+
+import subprocess
+import os
+
+# --------------- CHANGE THESE TWO LINES -------------------------
+OUTPUT_FILE = "Foo.pdf"
+
+#If you Reame the Header file let me know
+STU_HEADER_FILE = "Dissertation.md" #Students Header File
+
+#ENTER ALL THE SOURCE FILES THAT YOU HAVE IN THE DISSERTAION HERE.
+SOURCE_FILES = ["Example/Intro.md", "Example/Use.md"]
+
+#Are you using the Submodule Approach
+SUBMODULE = False
+
+#Is it the Default Path
+SUBMODULE_PATH="markdown-dissertation"
+# --------------- END OF STUFF THAT YOU NEED TO CHANGE -------------------------
+
+
+def buildCommand():
+    """Build the list that we send to pandoc"""
+    HEADER_FILE = "Header.md"
+    SUB_HEADER_FILE = "SubHeader.md"
+    #Needed otherwise refs come on the same page
+    FOOTER_FILE = "References.md" 
+    # Pandoc Template         
+    LATEX_TEMPLATE = "Template/disso.latex"
+
+    if SUBMODULE:
+        HEADER_FILE = os.path.join(SUBMODULE_PATH, SUB_HEADER_FILE)
+        FOOTER_FILE = os.path.join(SUBMODULE_PATH, FOOTER_FILE)
+        LATEX_TEMPLATE = os.path.join(SUBMODULE_PATH, LATEX_TEMPLATE)
+        
+    PANDOC_OPTS = ["--filter=pandoc-citeproc",
+                   "--template={0}".format(LATEX_TEMPLATE),
+                   "--top-level-division=chapter"]
+    
+    #Actually Build the list
+    commandList = ["pandoc"]
+    commandList.extend(PANDOC_OPTS) #Add the options
+    commandList.append(STU_HEADER_FILE) #Students Headderfile
+    commandList.append(HEADER_FILE) #Header File
+    commandList.extend(SOURCE_FILES) #STUDENT source 
+    commandList.append(FOOTER_FILE) #FOOTER FILE
+    commandList.append("-o")
+    commandList.append(OUTPUT_FILE)
+    print (commandList)
+    for item in commandList:
+        print (item)
+    subprocess.run(commandList)
+
+    
+if __name__ == "__main__":
+    #Build the damm thing
+    buildCommand()
diff --git a/Build.py b/Build.py
new file mode 100644
index 0000000..2a59ee3
--- /dev/null
+++ b/Build.py
@@ -0,0 +1,58 @@
+"""
+Python script to build a dissertaion based on Markdown / Pandoc
+
+TODO: Options?
+"""
+
+import subprocess
+import os
+
+# --------------- CHANGE THESE TWO LINES -------------------------
+OUTPUT_FILE = "Disso.pdf"
+
+#If you Reame the Header file you will need to let the script know.
+STU_HEADER_FILE = "Dissertation.md" #Students Header File
+
+#ENTER ALL THE SOURCE FILES THAT YOU HAVE IN THE DISSERTAION HERE.
+SOURCE_FILES = []
+
+#Are you using the Recommended Submodule Approach
+SUBMODULE = True
+
+#If you rename the Templates repository, Let the script know.
+SUBMODULE_PATH="markdown-dissertation"
+# --------------- END OF STUFF THAT YOU NEED TO CHANGE -------------------------
+
+def buildCommand():
+    """Build the list that we send to pandoc"""
+    HEADER_FILE = "Header.md"
+    SUB_HEADER_FILE = "SubHeader.md"
+    #Needed otherwise refs come on the same page
+    FOOTER_FILE = "References.md" 
+    # Pandoc Template         
+    LATEX_TEMPLATE = "Template/disso.latex"
+
+    if SUBMODULE:
+        HEADER_FILE = os.path.join(SUBMODULE_PATH, SUB_HEADER_FILE)
+        FOOTER_FILE = os.path.join(SUBMODULE_PATH, FOOTER_FILE)
+        LATEX_TEMPLATE = os.path.join(SUBMODULE_PATH, LATEX_TEMPLATE)
+        
+    PANDOC_OPTS = ["--filter=pandoc-citeproc",
+                   "--template={0}".format(LATEX_TEMPLATE),
+                   "--top-level-division=chapter"]
+    
+    #Actually Build the list
+    commandList = ["pandoc"]
+    commandList.extend(PANDOC_OPTS) #Add the options
+    commandList.append(STU_HEADER_FILE) #Students Headderfile
+    commandList.append(HEADER_FILE) #Header File
+    commandList.extend(SOURCE_FILES) #STUDENT source 
+    commandList.append(FOOTER_FILE) #FOOTER FILE
+    commandList.append("-o")
+    commandList.append(OUTPUT_FILE)
+    subprocess.run(commandList)
+
+    
+if __name__ == "__main__":
+    #Build the damm thing
+    buildCommand()
diff --git a/Dissertation.md b/Dissertation.md
new file mode 100644
index 0000000..cd1b508
--- /dev/null
+++ b/Dissertation.md
@@ -0,0 +1,24 @@
+---
+# ----- THINGS THAT YOU NEED TO CHANGE ----
+author:  "Your Name"
+title: "Project Title"
+
+# Keywords associated with your project
+keywords: Comma, Seperated, Keywords
+
+degreetitle:  'BSc: Ethical Hacking and cybersecurity'
+
+#Ethics form,  REPLACE THIS WITH YOUR ONE
+PDF-ethics: Supporting/ethics-certificate.pdf
+
+#Origianlity Statement:  REPLACE THIS WITH YOURS
+PDF-declaration: Supporting/submission-declaration.pdf
+
+#Finally the Bibtex file for your references.
+bibliography: example-bib.bib
+
+#Font to use
+fontfamily: helvet
+
+# -------- LEAVE THE THINGS BELOW HERE ALONE ----
+---
diff --git a/EG-Intro.md b/EG-Intro.md
deleted file mode 100644
index 31a87de..0000000
--- a/EG-Intro.md
+++ /dev/null
@@ -1,49 +0,0 @@
-# Introduction
-
-You can now replace this with whatever content you need,  I would have a file per section (as it looks nicer)
-Then modify the build.sh script to include the files in order.
-
-For example Original script looks like this
-
-~~~ bash
-#!/bin/sh
-
-pandoc 02-Originallity_Statement.md -o /tmp/02-Originallity_Statement.tex
-
-
-pandoc --template=Template/disso.latex --top-level-division=chapter --filter=pandoc-citeproc \
-       Frontpage.md \
-       01-intro.md \
-       References.md \
--o Dissertation.pdf
-~~~
-
-
-If you add a new file 02-LitReview.md  you need to modfy to be 
-
-~~~ bash
-#!/bin/sh
-
-pandoc 02-Originallity_Statement.md -o /tmp/02-Originallity_Statement.tex
-
-
-pandoc --template=Template/disso.latex --top-level-division=chapter --filter=pandoc-citeproc \
-       Frontpage.md \
-       01-intro.md \
-	   02-LitReview.md \
-       References.md \
--o Dissertation.pdf
-~~~
-
-
-
-
-This is a section
-
-## Subsections Should also work
-
-I hope very much
-
-[@goldsmith2010spanish]
-
-
diff --git a/Example/Intro.md b/Example/Intro.md
new file mode 100644
index 0000000..dcd9d8f
--- /dev/null
+++ b/Example/Intro.md
@@ -0,0 +1,38 @@
+# Introduction
+
+This template lets you write awesome looking Dissertations in Markdown.
+
+## Why would you want to do this
+
+ - It looks better
+ - You have nicer references
+ - You can use whatever tools you want to write (IE not stuck with Word)
+
+## Installation Instructions
+
+### Getting the Template
+TODO:  Instructions on Submodules etc here.
+
+First we want to download the Template, which can be found at <https://github.coventry.ac.uk/aa9863/markdown_dissertation>.  There are two options here:
+
+ 1. Clone my Repository
+ 1. Make use of Submodules to do it
+
+### Other Requirements
+
+You will also need a copy of:
+
+ - Pandoc
+ - LaTeX
+
+## Behind the Scenes
+
+Template is based on the (unofficial) Latex Coventry Universtiy Thesis
+template <https://github.com/GR8DAN/coventry-thesis>.
+
+Pandoc is used to convert from Markdown to text, with some custom
+export templates to glue everything together.
+
+It should work on Windows / Mac and Linux
+
+
diff --git a/Lorum.md b/Example/Lorum.md
similarity index 100%
rename from Lorum.md
rename to Example/Lorum.md
diff --git a/Example/Use.md b/Example/Use.md
new file mode 100644
index 0000000..fb409c6
--- /dev/null
+++ b/Example/Use.md
@@ -0,0 +1,73 @@
+# Using the Template
+
+## Step 1:  Modify the **Dissertaion.md** file.
+
+This file contains the metadata used to generate the title page etc.
+There isn't a huge amount that needs changing here, and it should be
+self explanatory.
+
+~~~ {.yaml}
+# ----- THINGS THAT YOU NEED TO CHANGE ----
+author:  "Your Name"
+title: "Project Title"
+
+# Keywords associated with your project
+keywords: Comma, Seperated, Keywords
+
+degreetitle:  'BSc: Ethical Hacking and cybersecurity'
+
+# Ethics form,  REPLACE THIS WITH YOUR ONE
+PDF-ethics: Supporting/ethics-certificate.pdf
+
+# Origianlity Statement:  REPLACE THIS WITH YOURS
+PDF-declaration: Supporting/submission-declaration.pdf
+
+# Finally the Bibtex file for your references.
+bibliography: example-bib.bib
+
+# Font to use (I would leave this)
+fontfamily: helvet
+~~~
+
+
+## Step 2: Create some Content
+
+You next need to create any content.
+I would recommend creating *One file per chapter*
+
+A Basic Markdown Primer can be found in [LINK]
+I am also putting together some docs on how I go about writing things
+
+## Step 3: Modify the Build script
+
+You will also need to modify the script that builds the dissertation **Build.py**
+As with the config file, there are only a couple of lines that you should need to change.
+
+ - Add any source files to the list of source files
+ - If you want, modify the name of the output file
+
+~~~ {.python}
+# --------------- CHANGE THESE TWO LINES -------------------------
+OUTPUT_FILE = "Disso.pdf"
+
+#ENTER ALL THE SOURCE FILES THAT YOU HAVE IN THE DISSERTAION HERE.
+SOURCE_FILES = ["EG-Intro.md"]
+# --------------- END OF STUFF THAT YOU NEED TO CHANGE -------------------------
+~~~
+
+## Step 4:  Build the Document
+
+We can now build the document using the script
+
+Either on the Command line.
+
+~~~
+python Build.py
+~~~
+
+Or by double clicking in you like Window Managers.
+
+## Optional:
+
+ - Commit all your files using Git
+ - Share the repository with your supervisor
diff --git a/Example/Writing.md b/Example/Writing.md
new file mode 100644
index 0000000..81182b2
--- /dev/null
+++ b/Example/Writing.md
@@ -0,0 +1,3 @@
+# Quick Markdown Primer
+
+Pandoc 
diff --git a/Frontpage.md b/Header.md
similarity index 57%
rename from Frontpage.md
rename to Header.md
index 96bbdea..9b4719a 100644
--- a/Frontpage.md
+++ b/Header.md
@@ -1,51 +1,35 @@
----
-author:  Your Name
-title: "Project Title"
-
-documentclass: Template/Classes/CUPhDThesis
-classoption:
-  - a4paper
-  - 10pt
-  - numbered
-  - print
-  - index
-  - oneside
-
-toc: true
-toc-depth: 2
-lof: true
-lot: false
-
-keywords: Comma, Seperated, Keywords
-
-
-fontfamily: helvet
-header-includes:
-   - \renewcommand{\familydefault}{\sfdefault}
-   - \renewcommand{\chaptername}{}
-   - \renewcommand{\thechapter}{}
-
-
-dept: 'Faculty of Enginnering and Computing'
-university: 'Coventry University'
-crest: 'Template/Figs/CULogo.pdf'
-degreetitle:  'BSc: Ethical Hacking and cybersecurity'
-
-#Ethics form,  REPLACE THIS WITH YOUR ONE
-PDF-ethics: Supporting/ethics-certificate.pdf
-
-#Choice of ither a printied and scanned Originality form
-#PDF-declaration: Supporting/submission-declaration.pdf
-
-#OR Nates, awesome Markdown one
-TEX-declaration: Supporting/OriginallityStatement.tex
-
-bibliography: example-bib.bib
-
-#Bibliograpy Style
-csl: Template/harvard-coventry-university.csl
-
-#If we are using biblatex instead
-biblatexoptions: backend=biber, style=authoryear, sorting=nty, natbib=true
-biblio-title:  "References"
----
+---
+documentclass: Template/Classes/CUPhDThesis
+classoption:
+  - a4paper
+  - 10pt
+  - numbered
+  - print
+  - index
+  - oneside
+
+toc: true
+toc-depth: 2
+lof: true
+lot: false
+
+header-includes:
+   - \renewcommand{\familydefault}{\sfdefault}
+   - \renewcommand{\chaptername}{}
+   - \renewcommand{\thechapter}{}
+
+
+dept: 'Faculty of Enginnering and Computing'
+university: 'Coventry University'
+crest: 'Template/Figs/CULogo.pdf'
+
+#Bibliograpy Style
+csl: Template/harvard-coventry-university.csl
+
+#OR Nates, awesome Markdown one
+#TEX-declaration: Supporting/OriginallityStatement.tex
+
+#If we are using biblatex instead
+biblatexoptions: backend=biber, style=authoryear, sorting=nty, natbib=true
+biblio-title:  "References"
+---
diff --git a/Makefile b/Makefile
index 2a08bf9..2d65697 100755
--- a/Makefile
+++ b/Makefile
@@ -5,8 +5,8 @@
 # If we have multiple inputs we we can stick them here
 # NOTE, It is important they are in order
 # Again we can pass this through the command line
-SOURCES = Frontpage.md EG-Intro.md Lorum.md References.md
-TARGET = Dissertaion.pdf
+SOURCES = Dissertation.md References.md
+TARGET = 
 
 #Report Export Options
 PDF_PANDOC_OPTIONS = --filter=pandoc-citeproc --template=Template/disso.latex --top-level-division=chapter
@@ -36,5 +36,5 @@ endif
 %.tex: %.md
 # Old way of doing it, now dealt with through target
 #	#pandoc $(PANDOC_OPTIONS) -o $@ $<
-	pandoc $(TEX_PANDOC_OPTIONS) -s $(SOURCES) -o Foo.tex
+	pandoc $(TEX_PANDOC_OPTIONS) -s $(SOURCES) -o $(TARGET)
 #$(TARGET)
diff --git a/SubHeader.md b/SubHeader.md
new file mode 100644
index 0000000..6da308c
--- /dev/null
+++ b/SubHeader.md
@@ -0,0 +1,35 @@
+---
+documentclass: markdown-dissertation/Template/Classes/CUPhDThesis
+classoption:
+  - a4paper
+  - 10pt
+  - numbered
+  - print
+  - index
+  - oneside
+
+toc: true
+toc-depth: 2
+lof: true
+lot: false
+
+header-includes:
+   - \renewcommand{\familydefault}{\sfdefault}
+   - \renewcommand{\chaptername}{}
+   - \renewcommand{\thechapter}{}
+
+
+dept: 'Faculty of Enginnering and Computing'
+university: 'Coventry University'
+crest: 'markdown-dissertation/Template/Figs/CULogo.pdf'
+
+#Bibliograpy Style
+csl: markdown-dissertation/Template/harvard-coventry-university.csl
+
+#OR Nates, awesome Markdown one
+#TEX-declaration: Supporting/OriginallityStatement.tex
+
+#If we are using biblatex instead
+biblatexoptions: backend=biber, style=authoryear, sorting=nty, natbib=true
+biblio-title:  "References"
+---
diff --git a/Supporting/submission-declaration.pdf b/Supporting/submission-declaration.pdf
new file mode 100644
index 0000000..368f84a
Binary files /dev/null and b/Supporting/submission-declaration.pdf differ
diff --git a/build.sh b/build.sh
index 789eccd..c15e60e 100755
--- a/build.sh
+++ b/build.sh
@@ -8,5 +8,5 @@ pandoc --template=Template/disso.latex --top-level-division=chapter --filter=pan
        EG-Intro.md \
        Lorum.md \
        References.md \
-       -o Dissertation.pdf
+       -o Dissertation.tex