improve documentation for new users

[lars2015]

Is your feature request related to a problem?

• new users need more detailed documentation to get started with MPTRAC

Describe the solution you'd like

• check/revise the README file
• revise and extend the mkdocs manual, including descriptions of individual apps/tools
• add/check links to references and other sources of information
• revise and extend the doxygen manual

Additional ideas

• implement `-help' flags in the apps
• create and add small logo for MPTRAC on doxygen and mkdocs manual

[hydrogencl]

Here I want to provide the solution to fix the documentation.
I change the path in the session of deploying_doxygen

from
publish_dir: ./docs/docs
to
publish_dir: ./docs/docs/html

since doxygen will generate the files in docs/docs/html

[lars2015]

• We need to update the documentation of the trac tool.

[fkhosrawi]

We also need to implement the comments and corrections from Jonas into the new version of the documentation and to improve the documentation of the control parameters, there are many missing in the doxygen list.