Add CLI notebooks to docs (#499)

* Move Python tutorials into separate directory

* Run singlepoint CLI notebook

* Run MD CLI tutorial

* Run geomopt CLI tutorial

* Run phonons CLI tutorial

* Run NEB CLI tutorial

* Store CLI tutorials

* Tidy tutorials

* Tidy CLI titles

Author: ElliottKasoar

docs/source/conf.py

@@ -109,7 +109,6 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # exclude_patterns = ['doc.rst']
-exclude_patterns = ["tutorials/cli/*.ipynb"]
 # ~ exclude_patterns = ['index.rst']
 
 # If true, sectionauthor and moduleauthor directives will be shown in the