Without major re-work I think it is unlikely to have it really fixed. This late in game development I think the chance to get changed is really slim.
Nevertheless...
Bobbing will be reduced by keeping the empire tree current line of ships aligned with the current mouse position.
The empire tree will not scroll around to follow the mouse, it will merely understand the line in which the mouse resides, and changes in ship groups should not make it bob up or down, but contents above and below the current line will be changed.
The whole point is to change the point of reference from 'top of empire tree' to 'current mouse vertical position'.
If the user moves the mouse vertically, the empire tree should not scroll up or down after it, it will just update which line the mouse is on, and attempt to keep it in place.
But changing the way its vertical position is calculated by tracking the current line of the ships and keeping it aligned with the mouse vertical position would be the way to go, IMO.
1. get current line (in the same horizontal line of the mouse).
1.1 keep current line aligned to mouse no matter what changes elsewhere.
1.2 if ships are flying to other gravwells all bobbing is gone.
Now, there is the problem of ships flying into the current gravwell, which will make the 6 ships in the 'current line' move right or left, and potentially change to the lines above/below, and without a clear definition this could cause bobbing. I think 2 rules are needed:
1. track the rightmost ship of the leftmost ship type.
if the line has mixed ship types, sticking with the leftmost will cope best with ships coming and going on the gravwell. If the user has the mouse in the border of 2 ship types, he is likely to be interested in either type, and microing.
If you just stick to the left ship, the ship types on the right might scurry away to the bottom if reinforcements arrive, and is most likely undesirable.
2. If there is a single ship type on the current line, attempt to keep the line filled with ships of this single type.
If there is a single ship type on the current line, the player is likely interested on this specific category.
Thus:
if ships coming and going would:
cause the right most ship on the current line to be of a different kind,
check if the line above only has ships of the kind we are interested at;
If true, jump tracking to the line above.
OR
cause the left most on the current line to be of a different kind,
check if the line below only has ships of the kind we are interested at;
If true, jump tracking to the line below.
And that is my idea.
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