Python/JS: Running CodeQL CLI against large datasets

**Description of the issue**

I'm currently trying to use CodeQL CLI to run a fixed set of queries against a very large number of individual JavaScript and Python files. These files are completely independent of each other, and any dependency linkage between the individual files would be a false positive.

Currently, I am breaking these files out into folders of a certain size and running `database create` and `database analyze` against each folder. But this process is very inefficient and it seems like many steps are redundant.

**Question**
How can I make this process as efficient as possible? For example, is there a way to clear a dataset and repopulate it with new files?