SCID is the software I use for the frontend. It lets me build a chess game the way I like to do it -- move by move, variation by variation, note by note. Because it recognizes PGN, which is essentially a text format, I can rearrange a game's components using a standard text editor. Unfortunately, SCID doesn't recognize chess960, but I have procedures to get around that limitation.
Arena is the software I use for the backend. It handles the details of running an engine. Whatever noteworthy results it discovers, I record using SCID.
Having two pieces of software means I have two copies of a game. The SCID version contains everything I've collected about the game, while the Arena version contains only what I need to analyze specific positions of interest. The advantage of being able to annotate and analyze simultaneously outweighs the slight disadvantage of maintaining two versions of a game.
The biggest challenge in switching to a new version of any software is to tailor it according to my preferences. This is never as easy as it should be and I didn't finish the job before completing this post. Looks like I'll be running the older versions of both SCID and Arena for at least a few more days.
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