manual tidy-up and add new ws and config introductory section

README.md

@@ -42,7 +42,7 @@ type:
 
 If you want the environment to be installed in another location, e.g. due to disk space limitations, type:
 
-    $ conda env create --file environment.yml --prefix some/other/location/for/cate
+    $ conda env create --file environment.yml --prefix some/other/location/for/dedop
 
 Next step is to activate the new environment. On Linux/Darwin type:
 
@@ -53,11 +53,11 @@ Windows users can omit the `source` command and just type
 
     > activate dedop
 
-You can now safely install and run Cate sources into the new `dedop` environment.
+You can now safely install and run DeDop sources into the new `dedop` environment.
 
     (dedop) $ python setup.py develop
 
-To permanently install Cate into the Python environment (not recommended while in development mode!), type:
+To permanently install DeDop into the Python environment (not recommended while in development mode!), type:
 
     (dedop) $ python setup.py install
 
@@ -82,11 +82,11 @@ If you like to perform L1B product analysis tasks with DeDop using an IPython No
 
 The most up-to-date and complete list of module requirements is found in the project's `environment.yml` file.
 
-To install and run Cate from sources directly, type:
+To install and run DeDop from sources directly, type:
 
     $ python setup.py develop
 
-To permanently install Cate into Python (not recommended while in development mode!), type:
+To permanently install DeDop into Python (not recommended while in development mode!), type:
 
     $ python setup.py install
 

docs/user_manual.rst

@@ -6,6 +6,7 @@ User Manual
    :maxdepth: 1
 
    user_manual/um_setup
+   user_manual/um_ws_and_config_concept
    user_manual/um_shell
    user_manual/um_studio
 

docs/user_manual/um_shell.rst

@@ -19,23 +19,14 @@ the DeDop Shell on your computer. See section :doc:`um_setup` for more informati
 Workspace Management
 ====================
 
-**Workspace** in DeDop Shell refers to a space in the file system in which all the requires parts for processing are located.
-They include source files, configurations, output files, as well as the Jupyter notebooks. It is possible to have multiple
-workspaces and by default they are located under ``$USER_DIR/.dedop/workspaces``.
-For example::
-
-   C:\\Users\\dummy_user\\.dedop\\workspaces  # Windows
-   /home/dummy_user/.dedop/workspaces         # Linux
-   /Users/dummy_user/.dedop/workspaces        # MacOS
-
 Add a new workspace
 --------------------
 
 When DeDop Shell runs for the first time, there is no workspace available. An automatic creation of default workspace can
 be triggered by running ``dedop input add some/path/to/your/L1A.nc`` or ``dedop run`` command as described
 :ref:`here <processing_l1a_l1b>`.
 
-Another (more recommended) way to add a new workspace is by running the following command::
+To add a new workspace is by running the following command::
 
    $ dedop w add workspace_name
 

docs/user_manual/um_ws_and_config_concept.rst

@@ -0,0 +1,53 @@
+===================================
+Workspace and Configuration Concept
+===================================
+
+Workspace
+==========
+
+**Workspace** in DeDop Shell refers to a space in the file system in which all the requires parts for processing are located.
+They include source files, configurations, output files, as well as the Jupyter notebooks. It is possible to have multiple
+workspaces and by default they are located under ``$USER_DIR/.dedop/workspaces``.
+For example::
+
+   C:\\Users\\dummy_user\\.dedop\\workspaces  # Windows
+   /home/dummy_user/.dedop/workspaces         # Linux
+   /Users/dummy_user/.dedop/workspaces        # MacOS
+
+When DeDop Shell runs for the first time, there is no workspace available. An automatic creation of default workspace can
+be triggered by running ``dedop input add some/path/to/your/L1A.nc`` or ``dedop run`` command as described
+:ref:`here <processing_l1a_l1b>`.
+
+Another (more recommended) way to add a new workspace is by running the following command::
+
+   $ dedop w add workspace_name
+
+Upon successful operation, the following responses shall be returned::
+
+   created workspace "workspace_name"
+   current workspace is "workspace_name"
+
+This means that the new workspace has been successfully created and made the current workspace, which means that, unless
+explicitly changed, whatever operations being performed after this will happen inside this workspace.
+
+Inside ``workspaces`` directory, there is a file called ``.current``, inside which the name of the current workspace can
+be found. When there is no current workspace (eg. because there is no more workspace after a deletion), this file will
+be empty.
+
+More information and example on workspace management operations, please go to :ref:`here <workspace_manag>`.
+
+Configuration
+==============
+
+**DeDop configuration** refers to a set of configurations (Configuration, Characterization, Constants), which in the file
+system are stored as CNF.json, CHD.json, and CST.json. Most of the time, users will need to modify only the **Configuration**.
+A configuration is represented by a directory with a name of the configuration name and is located under ``configs``
+directory inside a workspace directory. It is possible to have multiple configurations under each workspace and it is
+recommended to have a new configuration for different set of configuration values. This way, an output can be easily reproduced
+if needed in the future.
+
+As in ``workspaces`` directory, there is a ``.current`` file inside ``configs`` directory. It works following exactly the same
+concept: this file has the information on what is the current configuration. In the case of no current configuration,
+this file will be empty.
+
+More information and example on configuration management operations, please go to :ref:`here <config_manag>`.