Yes, the Scid Tree Mask does exactly this. Scid vs PC has some improvements to make the Mask more useable, and has rewritten help, but it still takes some getting used to/learning.
Create repertoire with programs - specific questions
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Ideally I would want to be able to annotate a position and save that annotation so that the annotation appears when that position is on the analysis board (not just in this game, but in general, like an opening book).
I've looked at the options SCID and the Arena GUI offer but I haven't found this option.
Are there any tools for this (free would be prefered), and if not, what would be the best way to get similar results?