Index: documentation/Sphinx/build/html/_sources/api.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/api.rst.txt	(revision 708c6674550abec09bd249f6654698bdeaed17d0)
+++ documentation/Sphinx/build/html/_sources/api.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -2,4 +2,81 @@
 ============================
 
+.. contents::
+    :local:
+    
+Porgrams
+--------
+
+install
+*******
+
+.. automodule:: install
+    :members:
+    
+submit
+******
+
+.. automodule:: submit
+    :members:
+    
+Classes
+-------
+
+ControlFile
+***********
+
+.. automodule:: ControlFile
+    :members:
+    
+EcFlexpart
+**********
+
+.. automodule:: EcFlexpart
+    :members:
+    
+GribTools
+*********
+
+.. automodule:: GribTools
+    :members:
+
+MarsRetrieval
+*************
+
+.. automodule:: MarsRetrieval
+    :members:
+
+UioFiles
+********
+
+.. automodule:: UioFiles
+    :members:
+
+
+
+Modules
+-------
+
+get_mars_data
+*************
+
+.. automodule:: get_mars_data
+    :members:
+ 
+prepare_flexpart
+****************
+
+.. automodule:: prepare_flexpart
+    :members:    
+    
+tools
+*****
+
+.. automodule:: tools
+    :members:
+
+disaggregation
+**************    
+    
 .. automodule:: disaggregation
     :members:
Index: documentation/Sphinx/build/html/_sources/downloads.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/downloads.rst.txt	(revision 708c6674550abec09bd249f6654698bdeaed17d0)
+++ documentation/Sphinx/build/html/_sources/downloads.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -5,2 +5,11 @@
  
     UNDER CONSTRUCTION
+    
+.. toctree::
+    :hidden:
+    :maxdepth: 2
+    
+    downloads/tar_balls
+    downloads/git_repo
+    downloads/history_changes
+    
Index: documentation/Sphinx/build/html/_sources/downloads/git_repo.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/downloads/git_repo.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/downloads/git_repo.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,4 @@
+Git Repository 
+==============
+
+  UNDER CONSTRUCTION
Index: documentation/Sphinx/build/html/_sources/downloads/history_changes.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/downloads/history_changes.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/downloads/history_changes.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,4 @@
+History of Changes
+==================
+
+   UNDER CONSTRUCTION
Index: documentation/Sphinx/build/html/_sources/downloads/tar_balls.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/downloads/tar_balls.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/downloads/tar_balls.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,4 @@
+Download tar-balls
+==================
+
+  UNDER CONSTRUCTION
Index: documentation/Sphinx/build/html/_sources/index.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/index.rst.txt	(revision 708c6674550abec09bd249f6654698bdeaed17d0)
+++ documentation/Sphinx/build/html/_sources/index.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -4,6 +4,17 @@
    contain the root `toctree` directive.
 
-Welcome to flex_extract's documentation!
-========================================
+Welcome to flex_extract's user documentation!
+=============================================
+
+flex_extract is a software to retrieve meteorological fields from the European Centre for Medium-Range Weather Forecasts (ECMWF) Mars archive to server as input files for the FLEXTRA/FLEXPART Atmospheric Transport Modelling system. 
+
+
+.. The scripts can be 1) executed locally using the ECMWF WebMARS interface, or 2) on the ECMWF member
+.. state gateway server or HPC facility using the ecaccess software package. As another option the scripts can 3)
+.. also be triggered using ecflow scheduling software used by ECMWF for data dissemination.
+
+All required second party software and libraries used within flex_extract is open source and free of charge. 
+
+
 .. raw:: html
 
@@ -87,5 +98,5 @@
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 3
    :caption: Table of Contents:
 
Index: documentation/Sphinx/build/html/_sources/installation.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/installation.rst.txt	(revision 708c6674550abec09bd249f6654698bdeaed17d0)
+++ documentation/Sphinx/build/html/_sources/installation.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -1,6 +1,15 @@
 Installation
 ============
-
-Describe installation process flex_extract ....
  
     UNDER CONSTRUCTION
+    
+.. toctree::
+    :hidden:
+    :maxdepth: 2
+    
+    installation/requirements
+    installation/oper_modes
+    installation/test_install
+
+
+    
Index: documentation/Sphinx/build/html/_sources/installation/oper_modes.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/installation/oper_modes.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/installation/oper_modes.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,6 @@
+Operating modes
+===============
+
+ 
+    UNDER CONSTRUCTION
+    
Index: documentation/Sphinx/build/html/_sources/installation/requirements.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/installation/requirements.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/installation/requirements.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,6 @@
+Requirements
+============
+
+ 
+    UNDER CONSTRUCTION
+    
Index: documentation/Sphinx/build/html/_sources/installation/test_install.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/installation/test_install.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/installation/test_install.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,5 @@
+Installation test
+=================
+
+    UNDER CONSTRUCTION
+    
Index: documentation/Sphinx/build/html/_sources/oper_modes.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/oper_modes.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/oper_modes.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,6 @@
+Operating modes
+===============
+
+ 
+    UNDER CONSTRUCTION
+    
Index: documentation/Sphinx/build/html/_sources/program_structure.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/program_structure.rst.txt	(revision 708c6674550abec09bd249f6654698bdeaed17d0)
+++ documentation/Sphinx/build/html/_sources/program_structure.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -5,2 +5,10 @@
  
     UNDER CONSTRUCTION
+    
+.. toctree::
+    :hidden:
+    :maxdepth: 2
+    
+    program_structure/prog_overview
+    program_structure/prog_components
+    program_structure/prog_flow
Index: documentation/Sphinx/build/html/_sources/program_structure/prog_components.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/program_structure/prog_components.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/program_structure/prog_components.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,5 @@
+Program Components
+==================
+
+ 
+    UNDER CONSTRUCTION
Index: documentation/Sphinx/build/html/_sources/program_structure/prog_flow.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/program_structure/prog_flow.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/program_structure/prog_flow.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,5 @@
+Program Flow
+================
+
+ 
+    UNDER CONSTRUCTION
Index: documentation/Sphinx/build/html/_sources/program_structure/prog_overview.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/program_structure/prog_overview.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/program_structure/prog_overview.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,5 @@
+Program Overview
+================
+
+ 
+    UNDER CONSTRUCTION
Index: documentation/Sphinx/build/html/_sources/requirements.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/requirements.rst.txt	(revision 708c6674550abec09bd249f6654698bdeaed17d0)
+++ documentation/Sphinx/build/html/_sources/requirements.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -2,5 +2,5 @@
 ============
 
-Describe the requirements to use flex_extract ....
  
     UNDER CONSTRUCTION
+    
Index: documentation/Sphinx/build/html/_sources/support.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/support.rst.txt	(revision 708c6674550abec09bd249f6654698bdeaed17d0)
+++ documentation/Sphinx/build/html/_sources/support.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -2,5 +2,15 @@
 =======
 
-Describe support options ....
  
     UNDER CONSTRUCTION
+    
+    
+.. toctree::
+    :hidden:
+    :maxdepth: 2
+    
+    support/ticket_system
+    support/mailing_list
+    support/known_bugs_issues
+    support/faq
+        
Index: documentation/Sphinx/build/html/_sources/support/faq.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/support/faq.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/support/faq.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,4 @@
+FAQ - Frequently asked questions
+================================
+
+  UNDER CONSTRUCTION
Index: documentation/Sphinx/build/html/_sources/support/known_bugs_issues.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/support/known_bugs_issues.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/support/known_bugs_issues.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,4 @@
+Known Bugs and Issues
+=====================
+
+  UNDER CONSTRUCTION
Index: documentation/Sphinx/build/html/_sources/support/mailing_list.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/support/mailing_list.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/support/mailing_list.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,4 @@
+Mailing Lists
+=============
+
+   UNDER CONSTRUCTION
Index: documentation/Sphinx/build/html/_sources/support/ticket_system.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/support/ticket_system.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/support/ticket_system.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,4 @@
+Ticket System
+=============
+  
+   UNDER CONSTRUCTION
Index: documentation/Sphinx/build/html/_sources/test_install.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/test_install.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/test_install.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,5 @@
+Installation test
+=================
+
+    UNDER CONSTRUCTION
+    
Index: documentation/Sphinx/build/html/_sources/user_guide.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/user_guide.rst.txt	(revision 708c6674550abec09bd249f6654698bdeaed17d0)
+++ documentation/Sphinx/build/html/_sources/user_guide.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -1,6 +1,12 @@
 User Guide
 ==========
-
-Describe using flex_extract ....
  
     UNDER CONSTRUCTION
+    
+.. toctree::
+    :hidden:
+    :maxdepth: 2
+    
+    user_guide/how_to
+    user_guide/control_templates
+    
Index: documentation/Sphinx/build/html/_sources/user_guide/control_templates.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/user_guide/control_templates.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/user_guide/control_templates.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,4 @@
+CONTROL-file templates
+======================
+
+   UNDER CONSTRUCTION
Index: documentation/Sphinx/build/html/_sources/user_guide/how_to.rst.txt
===================================================================
--- documentation/Sphinx/build/html/_sources/user_guide/how_to.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
+++ documentation/Sphinx/build/html/_sources/user_guide/how_to.rst.txt	(revision 274f9efe4b8438ab5238967e39adc200c624b56e)
@@ -0,0 +1,4 @@
+How to use flex_extract
+=======================
+
+   UNDER CONSTRUCTION
