Question

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So how exactly does SMO keep track of songs?
How does it know 'which' songpacks should be included and which shouldn't?
And how are two songs with identical names distinguished (if at all?)

[JunkoXXX]

it doesnt have it stored in packs on the server, if you have 2 songs with the same exact credentials but the chart its self and difficulty it will take you to the second installed song.

[foxfire667]

As I recall SMO just takes the info from SM and makes a page for it automatically when a new song is played.

Are you referring to the pack list and compare features? There isn't any filtering out of packs (though ones with no original songs can't exactly be detected right), it just hasn't really been updated since it's inception. I've uploaded a ton more content, and combed over things on the downloads page a bunch since then.

Two songs with identical names can be differentiated by their subtitles. If two files have the same name and subtitle, or no subtitle however, they are selected from as if they are the same. This is why if it puts you on the wrong one, you can navigate to the proper file and start it without SMO re-selecting the initial incorrect choice.