Seems like the type of thing that you would have needed to consider pretty early in the architecture of the application. At least to be done elegantly. You'd probably need the ability to have track entries that are "faux" (not mapped from a media file) metadata track entries that the app understands and will spider out to the real files/tracks behind the scenes whenever encountered in a playlist or whatever play context.
That might not be trivial at this stage. But yeah, I agree, the trickiest part would be crafting an intuitive UI around the feature.
Doesn't seem too difficult to me for either UI or playing. iTunes already supports this idea with their "grouping" tag (though it doesn't really do anything AFAIK). It doesn't need to be constantly visible in the UI. Being available with right click and "Get Info" is good enough for me. If you wanted more, you could add a "grouping" column to the view and a button on that column to collapse or un-collapse groups to appear as one track with the group name.
If you're shuffle playing and the next song in the queue has a non-empty group tag, remove it from the queue and instead add the whole group in the correct order. Everything else should be handled the same.
It might be a bad way of handling it (and if it is, I'd be glad to know why). But that's how I would implement such a feature.
So far my idea is that this would be exposed in the album view in the library - you could show line segments connecting songs which have been "grouped". This would make the state obvious and also provide a convenient way to multiselect and toggle grouping. Also when a song comes up solo (perhaps because the user chose to do so) since there is no where to draw a line segment to it would simply have a dot in a predictable location to indicate that it is missing its sister track.
Yeah I like the idea of representing the linkage as chain links.
Then you could show a broken chain link if a linked track is shown in a view by itself sans sibling(s).
That type of UI would be simple enough when you want to link tracks that appear in sequence on an album. Are there any use cases for the ability to link unrelated tracks X Y Z together? Probably not. Playlisting pretty much covers all that functionality.
Music players with cue sheet support kinda support the inverse of this. Throw a .cue into foobar and it will turn a whole album encoded as a single, giant .tta file (how I wish the Japanese knew of FLAC) into logically separate tracks. As I mentioned above, however, this isn't really necessary when album shuffle mode + a separate playlist solves the problem just fine on every existing music player.
That might not be trivial at this stage. But yeah, I agree, the trickiest part would be crafting an intuitive UI around the feature.