evals: Add system prompt to edit agent evals + fix edit agent (#31082)

1. Add system prompt: this is how it's called from threads. Previously,
we were sending
2. Fix an issue with writing agent thought into a newly created empty
file.

Release Notes:

- N/A

---------

Co-authored-by: Ben Brandt <benjamin.j.brandt@gmail.com>
Co-authored-by: Antonio Scandurra <me@as-cii.com>

Cargo.lock

@@ -688,6 +688,7 @@ dependencies = [
  "portable-pty",
  "pretty_assertions",
  "project",
+ "prompt_store",
  "rand 0.8.5",
  "regex",
  "reqwest_client",