Improved help experience (updated)

[themoenen]

(Adjusted version of PR #75)

In this pull request all issues listed in ticket #113

Mainly:

1. Splitting up our massive README.md file into separate pages per topic, i.e. installation, getting started, etc.

2. Updated the generate_docs() function to mirror the splitting up of our README onto the documentation website. All changes inside the /docs folder are related to this.

3. Various improvements to generate_docs() documentation website output, mainly much more usable "Commands" page and translation of GitHub alert tags:

Important

This is an important message

4. Added special README--PYPI.md for PyPI with all internal links translated to absolute links linking to docs website (TO BE TESTED ON NEXT UPDATE)

5. Support for querying command categories in the CLI, eg. ? molecule working set or mws ? will get you:

About your Molecule Working Set
-------------------------------
Your molecule working set (MWS) is an in-memory list of small molecules that is the subject of your calculations and manipulations.

The MWS makes it easy to gather candidate molecules from various sources, either by adding them individually, by loading them in batch from a 
dataframe, CSV or SDF file, or by bookmarking molecules in the GUI. You can then calculate certain properties, perform triage and then store 
the results in your workspace as a molecule set, ready for further processing within OpenAD or elsewhere.

Please note that at this time the MWS does not support macromolecules, only small molecules.


Molecule Working Set Commands
-----------------------------
add molecule|mol <name> | <smiles> | <inchi> | <inchikey> | <cid> [ as '<name>' ] [ basic ] [ force ]
remove molecule|mol <name> | <smiles> | <inchi> | <inchikey> | <cid> [ force ]
list molecules|mols
show molecules|mols
enrich molecules|mols with analysis
clear analysis cache
display sources <name> | <smiles> | <inchi> | <inchikey> | <cid>
rename molecule|mol <molecule_identifer_string> as <molecule_name>
load molecules|mols from file '<filename.molset.json|sdf|csv|smi>' [ enrich ] [ append ]
load molecules|mols from dataframe <dataframe> [ enrich ] [ append ]
merge molecules|mols data from dataframe <dataframe> [ enrich ]
export molecules|mols [ as '<filename.molset.json|sdf|csv|smi>' ]
clear molecules|mols [ force ]

[PhillipDowney]

Looking good, will need to test doco with LLM before launching new version.

[PhillipDowney]

changes accepted

[PhillipDowney]

Approved