Improve documentation

[efaulhaber]

This issue is to collect feedback that I got from students regarding the documentation.
I will continue this issue in the future with more feedback from more students/users.

1. using Pkg; Pkg.add("OrdinaryDiffEq", "Plots") doesn't work.
2. Add images of shapes to the docs (rectangle, sphere, etc.).
3. Add docs on how to visualize initial conditions for easier simulation setups.
4. Continue the method theory page and make it easier for users to find out which methods and corrections, density diffusion, boundary conditions are best for which use case.
5. Add more "developing TrixiParticles" information like best practices and conventions (format, comments, etc.).
6. Make clear that API reference is inside the components docs.