Fix and improve clear, remove and delete methods

[falkoschindler]

This PR attempts to solve #1512.
It is currently work in progress, extending the tests to unveil two issues with the current implementation.

Open tasks:

• let delete() correctly remove the element from its parent (test_delete_element)
• correctly call _on_delete() for all children of a removed parent (test_remove_parent)
• fix "RuntimeError: dictionary changed size during iteration"
• extend the documentation about clear(), remove() and delete()