Update the usage guide (#227)

* New "Ontology management" section that agglomerates several pages.

* Updated "Included ontologies" page.

* Dedicated page for `pico`. Removed related content from "Utilities" page.

* Updated "Working with ontologies" page and renamed to "Ontology packages".

* Moved supported ontology languages and formats to a new dedicated page.

* Removed YAML ontology format documentation, as it is not longed supported.

* Removed "Introduction to ontologies" section.

* Moved all pages from the "Working with Ontologies" sections to the usage guide.

* Changed title "Supported languages" to "supported formats" on supported_formats.md

* Remove the "Detailed design" section

* Update panels on the main page

* Replace ontology_interface.ipynb with terminological_knowledge.ipynb 

* Replace cuds_api.ipynb with assertional_knowledge.ipynb 

* Replace utils.md with visualization.ipynb (just a placeholder for now).

* Create dedicated section for sessions.

* Add introductory page to sessions.

* Add page on managing the session contents.

* Add page on queries using the session object.

* Add page on queries using the search module (WIP).

* Add page on queries using SPARQL (placeholder).

* Rename the import/export tutorial to RDF Import and export (no other changes yet).

* Remove sessions_and_vars.ipynb

* Remove multiple_wrappers.ipynb

* Create dedicated section for wrappers.

* Rename existing page to be the introductory page for wrappers (changes yet to be done).

* Move SimLAMMPS and Quantum Espresso wrapper pages.

* Add placeholder pages for wrappers included with SimPhoNy.

* Add page on queries using the search module.

* Add page on queries using SPARQL.

* Adapt the import/export tutorial to SimPhoNy v4.

* Add introduction (wrappers section).

* Fill SQLite wrapper page.

* Fill SQLAlchemy wrapper page.

* Fill Dataspace wrapper page.

* Fill Remote wrapper page.

* Remove Quantum Espresso tutorial.

* Remove SimLAMMPS tutorial.

* Hide the wrapper development tutorials (to be reincorporated later).

* Add visualization section.

Author: domgz

docs/detailed_design.md

@@ -36,26 +36,16 @@ SimPhoNy enables:
 
    Core functionalities, wrappers and advanced utilities
 
-   ```{link-button} jupyter/cuds_api.ipynb
+   ```{link-button} usage/ontologies/index.html
       :text: To the usage guides
       :classes: btn-outline-primary stretched-link
 
    ---
-
-   **Working with Ontologies**
-
-   Ontology overview, included ontologies, YAML ontologies and ontology querying
-
-   ```{link-button} ontology_intro.html
-      :text: To the ontology guides
-      :classes: btn-outline-primary stretched-link
-   ---
-
    **Wrapper Development**
 
    A deep dive into the wrapper mechanism for developing new wrappers
 
-   ```{link-button} wrapper_development.html
+   ```{link-button} wrappers/wrapper_development.html
       :text: To the wrapper development guides
       :classes: btn-outline-primary stretched-link
    ---
@@ -93,35 +83,34 @@ introduction/quickstart
 :caption: Usage Guide
 :maxdepth: 2
 
-usage/utils
-usage/cuds_api
-usage/sessions_and_vars
-usage/multiple_wrappers
-usage/import_export
-usage/simlammps
-usage/quantum_espresso
-```
+usage/ontologies/index
 
-```{toctree}
-:hidden: true
-:caption: Working with Ontologies
-:maxdepth: 2
+usage/terminological_knowledge
+usage/assertional_knowledge
 
-ontologies/ontology_intro
-ontologies/working_with_ontologies
-ontologies/ontologies_included
-ontologies/ontology_interface
-```
+usage/sessions/index
 
-```{toctree}
-:hidden: true
-:caption: Wrapper Development
-:maxdepth: 2
+usage/wrappers/index
 
-wrappers/wrapper_development_tutorial
-wrappers/wrapper_development
+usage/visualization
 ```
 
+# ```{toctree}
+
+# :hidden: true
+
+# :caption: Wrapper Development
+
+# :maxdepth: 2
+
+#
+
+# wrappers/wrapper_development_tutorial
+
+# wrappers/wrapper_development
+
+# ```
+
 ```{toctree}
 :hidden: true
 :caption: API Reference
@@ -136,7 +125,6 @@ api_reference
 :maxdepth: 2
 
 contribute
-detailed_design
 links
 license
 Data protection <https://www.simphony-project.eu/en/data_protection.html>