Save aequilibrae project directly from qgis

[r-akemii]

This PR modifies the qaequilibrae.py file to allow saving AequilibraE project directly from QGIS, without having to activate the command via plugin.

Related tests and documentation files were also updated and/or removed.

[pedrocamargo]

@r-akemii , the only thing we are missing is a clear note in the documentation saying that saving a QGIS project automatically saves the AequilibraE project. That is too good of a feature to not brag about