Check that each added substrate has a unique name. Same for parameters (for a given type).

Also, clean up some code to improve maintainability/readability.

Suggestion for future improvement: rename some of the many instances of "parameters" in the code. For example, UserParameters has one instance called parameters. Each instance of Parameters has a member called parameters. Many other objects in PhysiCell have parameters members. This makes it hard to track which ones belong where.