Update the usage guide

[kysrpex]

• 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.

[kysrpex]

@pablo-de-andres The whole PR is not ready but all sections in the usage guide from the beginning up to "Queries: using the session object" can be reviewed.