How to best manage a large and growing collection of tools is something I've been fighting with a lot recently.

I am currently finding that progressive discovery via something like a Tools table in SQL might be the best option. The "compression" ratio achieved here can be extreme. You could have a million tools and as long as only a handful match the query each time, it still wouldn't overwhelm the context window. You can also add biz rules to this process. For example, you can force the agent to further constrain its tool search if too many rows are returned.