Resolve "Add AbstractPort" and "Change Port ID to Port Index"

• Changes the port module by introducing a fully abstract "Port" interface and then an "AbstractPort" abstract class that implements the Port interface, which is in line with the class diagram.
• Renames many functions such as "connect_port" to "connect" and "connect_signal" to "add_signal" for better useability and to fit with the class diagram.
• Moves "AbstractGraphComponent" to the graph_component module.
• Also renames functions such as "connect_source" to "set_source" in signal.
• Refactors Port ID to Port Index as in #49 (closed)
• Move AbstractOperation implementation to the operation module.
• Mode BFS implementation from the utilites module to the operation module to solve cyclic imports.

Closes #48 (closed) Closes #49 (closed)