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Improve setting rename/migration functionality (#96)

* Improve setting rename/migration functionality

The previous mechanism for implicitly renaming old setting names to new
ones lived in settingsRules, which are difficult to extend from plugins.
As a result there were still a bunch of RENAMES for settings that have
since been removed from ARMI altogether. This includes a handful of
changes that allow these renames to live closer to the Settings to which
they apply, and therefore accessible to plugins. Changes include:

 - Introduction of ArmiPluginManager. This is a subclass of the pluggy
 version, which adds a counter that is incremented any time the set of
 registered plugins changes. This allows clients to safely cache things
 derived from the plugins, and invalidate those caches as necessary. We
 may instead want to go the route of simply locking the plugin manager
 and preventing future modification, but this should work well for now,
 and is more flexible.

 - Add getSettings() method to the App class. The corresponding logic
 used to be called through the Settings.__init__() method, which was
 pretty odd.

 - Add the oldNames instance attribute to the Setting class. This is
 used to handle setting renames in lieu of settingsRulese.RENAMES.

 - Add the SettingRenamer class to settingsIO, which distills the
 oldNames from the Setting instances and helps settingsIO perform
 migrations

 - Merge the protected and public sections of SettingsReader. This was a
 holdover from when the SettingsReader doubled as a setting definition
 reader as well, and now only served to complicate matters.

 - Migrate the contents of RENAMES to their respective settings

* Address reviewer comments

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