

I think SQLite is a great middle ground. It saves the database as a single .db file, and can do everything an SQL database can do. Querying for data is a lot more flexible and a lot faster. The tools for manipulating the data in any way you want are very good and very robust.
However, I’m not sure how it would affect file size. It might be smaller because JSON/YAML wastes a lot of characters on redundant information (field names) and storing numbers as text, which the database would store as binary data in a defined structure. On the other hand, extra space is used to make common SQL operations happen much faster using fancy data structures. I don’t know which effect is greater so file size could be bigger or smaller.
True (in most contexts, probably including this one), but I think that only makes the case for SQLite stronger. What people do still care about is a good flexible, usable and reliable interface. I’m not sure how to get that with YAML.