update the structure of the documentation, adding one file per submodule in the pheromone_dispersion and source_localization modules

update the configuration of sphinx, especially add intersphinx_mapping for reference to numpy and scipy

improve readibility of the method minimize by moving all the initialization part into the methods cold_start and hot_start, and moving the method save_output out of the method minimize as well

update the documentation of the gradient_descent module to the Docstring NumpyDoc format, and minor updates

update the documentation of the adjoint_convection_diffusion_2D module to the Docstring NumpyDoc format