Almost everything in .cogs/ is a table. The main exception is formats.json but I think that could fit into a table with two columns: format ID and the format JSON.
Would a cogs.db file be better than a .cogs/ directory? I'm finding myself using multiple Google Sheets for a given project, so I make various subdirectories each with their own COGS setup: foo/.cogs/ and bar/.cogs/. Maybe multiple .db files would be better? cogs foo.db add baz.tsv, cogs foo.db push
Changing over would be a pain, so we'd want a big win, and this doesn't seem big enough.