[Scenario] Resolve Save All/Refresh issue

Addressed are two issues:

* nasa/MCT-Plugins#72 is addressed by utilizing the capabilities defined in nasa/mct#206 to explicitly mark changed activities (including those exposed by way of collections) as modified for subsequent Save All actions
* nasa/MCT-Plugins#56 (remaining work) is addressed by moving the stale listener to a common super class of Scenario and Timeline, such that both exhibit the same "rebuild on staleness" behavior.