Improve documentation markdown files

[brookwander]

Use cases:

1. Adding info for people who are using catlas outside of "normal operation"

Scope:
What will be done:

1. Make an item in advanced use to include making a bulk db
2. Making documentation describing how to compare catlas against custom DFT (to be run by user)
3. Making documentation for what to do when your adsorbate is ood (making a custom pkl file)

What will not be done:

1. Any actual coding to support the above points

Execution plan:
All to be done solo by Brook. This is a low priority item.

Consider any problems / risk:
None! Just documentation