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How do these old games get discovered? Are they included in ancient game commentaries, hardly anybody has seen?
There's obviously a variety of ways, but the three most typical are:
(1) Handwritten copies made by pros who stay with go fans in remote places who have well-stocked libraries. Iwamoto Kaoru was perhaps the most prolific in this respect, but, before the days of photocopying, it was normal for many pros to do this sort of thing. But their papers often only come to light many years after their death.
(2) Related to that, private families often have heirloom libraries but their current owners aren't interested in go (and/or often can't read the old texts!). It's often just a chance encounter that brings these to light. For example, a title match may be held in some obscure rural spa, and the local publicity stimulates people into looking in the lofts and libraries.
(3) Quite a few go pros are avid collectors of old books. In the case of the Shuwa Castle Game, we can thank Yamazaki Masuo, who died in 2000. He has described as being interested in go culture more than in playing tournaments, although he did reach 7-dan in the Nihon Ki-in, and the found the Shuwa game in a book he found while browsing in the Kanda old-books area of Tokyo. Been there, done that!
Another but minor source is when a local historian takes an interest in a historical player who came from his area. This is essentially how most of the recent Yasui Chitoku discoveries were made.
But the person we most have to thank at present is go pro Fukui Masaaki, who is in his seventies now but seems even more active in this field than before. He specialises in Edo go and has published in various places. I suppose he might well have been inspired in this by Iwamoto, who was his teacher.
It's a similar situation in China and Korea, of course, and quite a lot has appeared from China recently. For example, some new games of Huang Longshi, which I added to GoGoD in a previous update. I have lots (?hundreds) more old Chinese games, and also more historical sunjang baduk games, but finding time to transcribe them is difficult - and not very appealing in a western world where 99.9% of go players are interested only in AI and numbers!