Add more descriptions to tutorials, update links to base code

[marjanalbooyeh]

This PR addresses some comments in this JOSS review.

Comments

• In the tutorials, the authors repeatedly refer the user to the source code of the different classes for examples (i.e. Pack and Lattice). That should not be the case. Examples of using the different classes should be available in the documentation or the tutorial.
• In tutorial 2, The authors provide examples of how to create a custom molecule. In example 4, they mentioned that a custom molecule can be defined through a class. The authors should give a concrete example of the required attributes of that class and how to define the molecule instead of just referring to the source code.
• I found it very good that you can define your force field using .xml files. However, I think the authors need to specify how the .xml file should be constructed or re-direct the interested user to a reference with that information.

Fix:

• Updated the text and added more description/instructions on subclasses.
• I added links to the flowemd documentation replacing links to the code base.
• Added a link to foyer xml sample format

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[chrisjonesBSU]

LGTM! Thanks @marjanAlbouye