Add documentation for the command-line scripts

[rwxayheee]

Preview of the edited documentations: https://rwxmeeko.readthedocs.io/en/latest/cli_rec_prep.html#

Please consider the added documentations a basic version for the command-line scripts.

For each command-line .py scripts, the documentation has three main sections:

(1) A very brief summary and a code block as the Basic usage

(2) An About section that allows us to explain the design and the importance, like the Templates, Write flag and the Residue selection and assignment language for mk_prepare_receptor.py

(3) An exhaustive list of Options. This list is generated not manually written. could add some more details and example usage for the most commonly used options.

@diogomart Please let me know if you like the layout, and I could add more details to the description pages of the command line scripts! Thanks

Some other changes included in this PR:

• Deleted the redundant Table of Content in the body of tutorials

• Deleted installation of Meeko from tutorials

• Added the Covalent (Tethered) Docking Colab back. The two Colab notebooks now use a better (complied from develop) version of AD-GPU

• Some other small fixes

[diogomart]

Thanks a lot for this. This helped a lot! In #229 I reorganized the left side bar. I didn't include the last three commits herein to avoid bringing a large number of files from the tutorials repository, but the other commits were included. I'll close this as #229 will merge most of this PR.