[doxygen] Add instructions from clean-up for 3.0 release

doc/doxygen/README.md

+Please follow these instructions when commenting your code for the Doxygen class documentation.
+When checking doxygen, the doxygen should be built and the doxyerr.log should have as little lines/errors as possible.
+
+The Doxygen for a **file** should look like this:
+```
+/*!
+ * \file
+ * \ingroup Common
+ * \brief Manages the handling of time dependent problems
+ */
+```
+It should always contain the `\file` first.
+The `\ingroup` gives a Group that is as **precise** as possible and is part of the `modules.txt`
+The `\brief` is a **short comment**  on what happens in the file. Alternatively a `\copybrief` could be used. **Make sure the copybrief links to the correct section and is not ambigous!**
+Additional text could be added similar to the function description.
+
+A class could look like this:
+
+```
+/*!
+ * \ingroup Common
+ * \brief Manages the handling of time dependent problems.
+ *
+ * This class facilitates the time management of the simulation.
+ * It doesn't manage [...]
+ * [...]
+ * [...] index starting at 0.
+ *
+ * \note Time and time step sizes are in units of seconds
+ */
+```
+The class should always have the proper `\ingroup` just like the file.
+The `\brief` should always contain a **short description**, and only in very very rare occasions a class can have a `\copybrief`. In the end this is also documentation for users that do not build doxygen and `\copybriefs` from another file are most likely not very useful.
+The main part should be an in depth explanation of what is done. This should contain math-expressions where applicable. They can look like the following:
+```
+ * This class implements a spline \f$s(x)\f$ for which, given \f$n\f$ sampling
+ * points \f$x_1, \dots, x_n\f$, the following conditions hold
+ *\f{align*}{
+   s(x_i)   & = y_i \quad \forall i \in \{1, \dots, n \}\\
+   s'(x_1)  & = m_1 \\
+   s'(x_n)  & = m_n
+   \f}
+*
+```
+
+For a **function** in a file the Doxygen can look like this:
+
+```
+/*!
+ * \brief Set the current simulated time and the time step index.
+ *
+ * \param t The time \f$\mathrm{[s]}\f$ which should be jumped to
+ * \param stepIdx The new time step index
+ */
+ void setTime(Scalar t, int stepIdx)
+     { time_ = t; timeStepIdx_ = stepIdx; }
+```
+The function has a **short comment** with the `\brief`.
+If there are **function-arguments** that are not self-explanatory, they should be described using `\param`.
+**Always explain all params or no params at all!** Otherwise Doxygen will throw an error.
+Template parameters are documented with `\tparam`.
+Additional Doxygen-commands that might be useful are `\note` for giving an important note/hint on what the function does as well as `\return` which specifies the return value (if applicable).