Add info about counting variables in callbacks

[maxhoerstr]

Closes #14.

Changes:

• Add input parameters to Service API and Task API classes which are deep copies of the corresponding input parameters of the model classes
• Substitute all counting variables in the API classes (for example, if a task is started 3 times in a loop, do not provide the variable "i" in each callback, instead provide the ith iteration step, so 0, 1, 2
• Add deep copy methods in Struct and Array, as they are used in the input parameters
• Implement unit tests for the deep copy methods
• Fix a problem where the parallel loop would not be properly started if it were the first statement in a task