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Addressed several code smells related to custom processes
Changes include: - Made several `protected` data members `private`. Added getter functions to access them when needed. - Replaced some explicit type names by `auto`. - Declared some member functions `const`. - Changed a parameter type to a reference-to-const. - Removed an overridden member function since its body was identical to the base class implementation. - Use a range-based for loop rather than an index to iterate a vector. - Added a `static_cast` to avoid a difference in signedness. - Initialized a pointer when it is declared. Also moved the declaration closer to its first usage. - Reformatted most changes using Clang-format. - Rephrased a comment. - Renamed several variables/function parameters. These were not compliant with the Kratos Style Guide.
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