I'm looking to analyze the backed up DB file and was wondering if there was a table by table guide to the schema.
No.
Kindling is open source and has some reference code you could follow to see general well-known structures, but because any module(s) you have could be adding or interacting with any number of tables, plus any tables could have any number of deprecated values depending on version, any documentation we provide is just going to be a bug-for-bug duplicate of whatever the software is already doing, which means it's a maintenance nightmare.
Thanks for Kindling!
Is there a CLI/API to it, or no?
No, unfortunately I made the mistake early on of not really separating the data model from the GUI; in most cases they're pretty inextricably linked. In past me's defense, I wasn't (and still am not sure) exactly how a CLI or other presentation for the data would actually work; the whole point of Kindling is to be an interactive tool you work with, not really a set-and-repeat mechanism.
Well, specifically what I care about is having the ability to run queries over the IDB, which would be enough for me. Agreed in other ways it's challenging.
The IDB is SQLite. Use the CLI for SQLite. Or one of its APIs. Use Kindling's source code as guidance on what to query.