Clean examples -- CLI protein-ligand example for Tyk2 (#1223)

* Improving examples dir structure and readme

* Adding Tyk2 CLI example

* removing new-cli/ripk2 example (deprecated)

* fix typo for link

* Clarify tyk2 cli example docs

examples/README.md

@@ -1,11 +1,16 @@
 Examples
 ========
-This directory contains examples of expanded ensemble simulations using various methods.
+This directory contains examples of the different modules in perses that can are used expanded
+ensemble simulations using various methods.
 
-Example types
--------------
-* rjmc - Examples using the Reversible Jump MCMC framework
+Subdirectories
+--------------
+The examples are organized in subdirectories as follows. More information on each example in the `README` files inside
+each subdirectory.
 
-* multitopology - Examples which use the multitopology-based framework
-
-* dualtopology - Examples using dual topology tools
+* [`atom-mapping`](atom-mapping) - Notebooks and script with examples on how to use perses atom mapping capabilities.
+* [`barnase-barstar-neq-switching`](barnase-barstar-neq-switching) - FE estimate using NEQ switching in protein:protein barnase-barnase complex.
+* [`dipeptide-neq-switching`](dipeptide-neq-switching) - Alanine dipeptide mutation using NEQ switching.
+* [`kinase-neq-switching`](kinase-neq-switching) - NTKR1 kinase protein-ligand FE simulation using NEQ cycling
+* [`moonshot-mainseries`](moonshot-mainseries) - Scripts used to prepare simulations to run with perses CLI for the COVID Moonshot
+* [`protein-ligand-repex`](protein-ligand-repex) - Tyk2 protein-ligand benchmark Replica Exchange simulation examples, using perses CLI.