Remove unneeded escapes in documentation source files

[akohlmey]

Summary

• replace \_ with _ in documentation sources where possible for easier editing
• some more code blocks
• resolve a few formatting issues uncovered by the changes in this PR
• includes and thus closes Add special highlights for commands which use IDs #1939

Author(s)

Axel Kohlmeyer (Temple U)

Licensing

By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).

Post Submission Checklist

• The feature or features in this pull request is complete
• Licensing information is complete
• Corresponding author information is complete
• The source code follows the LAMMPS formatting guidelines
• Suitable new documentation files and/or updates to the existing docs are included
• The added/updated documentation is integrated and tested with the documentation build system

[akohlmey]

@rbberger this is a version of the manual with all \_ removed except for a few cases that have "f\_" or "c\_" or "v\_" or "d\_", where this is not allowed. Please check it out and see if you can find some issues. This would make editing and reading the RST format sources significantly easier.