Don't clear AiSequence if there are no saved packages (eg for old savegames)
Fix triggering changed flag for all references when cell is visited

The InsertFunctor for cells was calling localRotateObject() for all references which set the mChanged flag in RefData to true.

Also clean up RefData interface slightly.
Fix incorrect trigger of change flag for static doors
Consider moved references in CellStore::listRefs
Move AiWander arrival check to time-critical section
Remove a squareroot in pathfinding
Don't allow scripted dialogue with dead actors (Fixes #1493)
Sort using ciLess, not ciEqual
Disable all other animations on death (Fixes #1483)
Clear message boxes in windowmanager cleanup (Fixes #1496)
Don't run scripts when in pause menu (Fixes #1495)
Implement BetaComment instruction (dumps reference info)
Fix some doxygen typos
Disable fProjectileThrownStoreChance when shooting at player (Fixes #1490)
Savegame: Store AiSettings and summoned creatures

CreatureStats state is now completely stored (Closes #1174)

Also play VFX_Summon_Start and VFX_Summon_End visual effects.
Make ESM::Faction skills optional (Fixes #1508)

Also increased size of mSkills array to 7. Some factions with 7 skills can be found in the vanilla CS. The previously "mUnknown" int appears to be the 7th element of the skills array.
Make Bipedal creatures always able to walk and swim (Fixes #1509)

This is necessary since the vanilla CS greys out the walk/swim checkboxes when Bipedal is checked.
Attempt to open companion window if no greetings are found (Bug #1507)
Add items to player inventory upon drag start (Fixes #1507)
Clear MyGUI's clipboard, since we don't want to use it (Fixes #1277)

This would cause pasted text to appear twice, but only when using an SVN version of MyGUI, since 3.2 had a bug where it wouldn't recognize the Ctrl C/V/X keys when using separated key/textinput events.