Modernize user guide (#4504)

Description of changes:
* use the *Alabaster* theme
   * responsive theme for mobile and tablets
   * visually light theme with consistent font sizes
   * natbib-style bibliography
* re-organize the user guide
   * collect information about running ESPResSo simulations into a self-contained chapter
   * move electrokinetics and reaction methods to self-contained chapters
   * make code examples more self-contained and remove pseudo-code
   * combine all BibTeX files into a single file
   * document running simulations in parallel with MPI
      * follow-up to mailing-list messages [Parallelization](https://lists.nongnu.org/archive/html/espressomd-users/2021-12/msg00011.html) and [max number of CPU's](https://lists.nongnu.org/archive/html/espressomd-users/2022-01/msg00001.html)

CONTRIBUTING.md

@@ -3,69 +3,71 @@
 
 Thank you for your interest in contributing to ESPResSo! There
 are many ways to contribute and we appreciate all of them. This
-document is a quite lengthy, so here is a list of links to the
+document is quite lengthy, so here is a list of links to the
 major sections:
 
 * [New Features](#new-features)
 * [Bug Reports](#bug-reports)
 * [Pull Requests](#pull-requests)
 * [Writing Documentation](#writing-documentation)
-* [Helpful Links and Information](#helpful-links-and-information)
 
-If you have questions, please make a post on [the developers
+If you have questions, please make a post on [the users
 mailing list][mailing-list].
 
-[mailing-list]: https://lists.nongnu.org/mailman/listinfo/espressomd-devel
+[mailing-list]: https://lists.nongnu.org/mailman/listinfo/espressomd-users
 
 ## New Features
 [new-features]: #new-features
 
 If you plan to create a new feature for ESPResSo, it is
-*absolutely essential* that you first post your plan on [the
-developers mailing list][mailing-list].  This way we can give you
-useful tips how to go about a successful integration and can
+*absolutely essential* that you first post your plan on the
+[users mailing list][mailing-list].  This way we can give you
+useful tips on how to go about a successful integration and can
 point out possibly reusable code.  Maybe your feature even exists
 already and you just didn't notice it, so we want to save you the
 effort.
 
 ## Bug Reports
 [bug-reports]: #bug-reports
 
-We cannot fix bugs we don't know about, so please report
-liberally. If you are unsure whether something is a bug or not,
-feel free to file a bug anyway.
+We cannot fix bugs we don't know about, so please report liberally.
+If you are unsure whether something is a bug or not, feel free to
+ask on the [users mailing list][mailing-list] or on the
+[discussion forum](https://github.com/espressomd/espresso/discussions).
 
 To fix your problem quickly it is essential that we have an easy
 way to reproduce your bug.  Therefore you should include in your
 report the *desired behavior*, a *specific problem or error* and
-*the shortest script necessary* to reproduce it.  Ideally you
-also include the affected version and list of features activated
-in `myconfig.hpp`.
+*the shortest script necessary* to reproduce it.  We have handy
+step-by-step instructions in the wiki page [Filing bug reports
+](https://github.com/espressomd/espresso/wiki/Filing-bug-reports).
 
 ## Pull Requests
 [pull-requests]: #pull-requests
 
-Pull requests are the primary mechanism we use to change
-ESPResSo. GitHub itself has some [great documentation][pull-requests]
+Pull requests are the primary mechanism we use to change ESPResSo.
+GitHub itself has some [great documentation][gh-pull-requests]
 on using the Pull Request feature.  We use the "fork and pull"
-model [described here][development-models], where contributors
+model [described here][gh-development-models], where contributors
 push changes to their personal fork and create pull requests to
 bring those changes into the source repository.
 
-[pull-requests]: https://help.github.com/articles/about-pull-requests/
-[development-models]: https://help.github.com/articles/about-collaborative-development-models/
+[gh-pull-requests]: https://help.github.com/articles/about-pull-requests/
+[gh-development-models]: https://help.github.com/articles/about-collaborative-development-models/
 
 Please make pull requests against the `python` branch.
 
-We have a continuous integration system for automated testing,
+We have a continuous integration system for [automated testing](
+https://github.com/espressomd/espresso/wiki/Code-review#automated-code-review),
 which runs on all pull requests to see whether new additions play
 nicely with the existing code.  Because it takes a long time for
 all the tests to be completed, you might want to run `make check`
 with the settings from `maintainer/configs/maxset.hpp` locally
 first.
 
 All pull requests are reviewed by one or more of the ESPResSo
-core team members.
+core team members, as explained in the wiki page [Code review
+](https://github.com/espressomd/espresso/wiki/Code-review#Human_code_review).
 
 ## Writing Documentation
 [writing-documentation]: #writing-documentation