SDK: Added alert dialog, more settings for individual dialogs

(integrated from master branch change 879818b by Nathan Rijksen <n.rijksen@gmail.com>)
UI: added "special" color to scheme skinning

(integrated from master branch change 7d1e367 by Nathan Rijksen <n.rijksen@gmail.com>)
SDK: Added file and prefs modules

(integrated from master branch change d377cda by Nathan Rijksen <n.rijksen@gmail.com>)
Commando: Various enhancements

- Added shortcuts to files scope
- Manually handle focus
- Added file renaming, copying, moving
- Removed onShow from scopes (queries are no preserved when reopening
commando)

(integrated from master branch change 1829cf7 by Nathan Rijksen <n.rijksen@gmail.com>)