Improve data entry point for simulator as a lib

[JasonMarechal25]

Currently the only entrey point possible to use simulator as a library is Application::prepare(int, char*[])

This signature suppose to pass parameters as if taken from a CLI, with argv[0] being a name for the program and so on.

Another issue is that simulator fills two data structures from CLI options and mutate the values of those structures afterwards.

The goal is to provide a single structure (or meta structure) to the entry point. This structure can be filled by a client or by simulator main after CLI parsing. The structure is unmutable and the current mutation will take place in a second, dedicated structure.