One trick I've found that works well is to tell it to refactor, e.g for Python:

    Refactor the Python code to make it more Pythonic, e.g. fewer classes/singletons, especially if it will provide a speedup. The Python code **MUST** follow code organization standards expected of popular open-source Python packages code without causing any benchmark performance regressions.

A variant I've used for Rust code:

    The Rust codebase in `/src` has become bloated with several files >1k LoC. Refactor the Rust codebase to fit code organization standards expected of popular open-source Rust code without causing any benchmark performance regressions.

Those types of prompts appear to a) reorganize the code logically and b) do seem to get better performance from the agents because the file names now provide semantic hints to where relevant code resides. For bloated 5k LoC files, the agent has to Read several chunks to find relevant code which is inefficient.

In terms of benchmark performance it generally improves after the refactor which I suspect is coincidental (especially in Rust where it shouldn't matter due to compiling) but I'm not complaining.