Add writer style option to SettingsWriter pt1

[opotowsky]

NOTE: the updates to the original PR on this topic requested by @keckler will be in a follow-up PR, namely making this argument available to clone / writeInputs.

Description

As described in Issue #897, we would like a third option that preserves the original settings file even if a setting defined in it is a default value. Currently, short removes all settings that have the default value, and full prints out every possible setting to the file.

To accomplish that, I added a medium style option to SettingsWriter (which involved editing the handling of the strings of "acceptable" styles to constant strings as well as a helper function in the caseSettings module called getSettingSetByUser so the full list of user defined settings can be tracked.).

I made the settingsWriteStyle flag available to the modify EntryPoint, so one can alter the writing style from the command line.

The testing was a little difficult. writeToYamlFile method and SettingsWriter class aren't explicitly tested. I have the 3 writing style options tested, the new method (getSettingsSetByUser) in caseSettings.py is tested, and a sad attempt at adding this to the modify CLI testing.

---

Checklist

• This PR has only one purpose or idea.
• Tests have been added/updated to verify that the new/changed code works.

• The code style follows good practices.
• The commit message(s) follow good practices.

• The release notes (location doc/release/0.X.rst) are up-to-date with any bug fixes or new features.
• The documentation is still up-to-date in the doc folder.
• The dependencies are still up-to-date in setup.py.

[keckler]

Beautiful. I love it. Only a few very piddly comments.

[john-science]

I love the test coverage!