Config Parser Fixes

There are several minor issues with the parser.

## Lists have redundant nesting.



Despite the fact that a list is a parameter value, the parser detects first detects it as a nested parameter (created as a hashMap)

**Intended:** If a parameter's value is a list, it should not be treated as a nested ParameterArray.

## Parsing Bugs

There are still numerous bugs lurking within the parser. Here are two examples found in `Brandish` config.



## Refactoring
The code is in **dire** need of proper refactoring.

Start by locating the configuration parser and reproducing the examples from the Brandish config mentioned in the issue. Investigate why list-valued parameters become nested ParameterArray or hashMap structures. Done means list values parse without redundant nesting and the reported parsing examples produce the intended results; the requested refactoring scope is not defined.

Written by the indexing model from the issue text.