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>

crates/assistant_tools/Cargo.toml

@@ -41,6 +41,7 @@ open.workspace = true
 paths.workspace = true
 portable-pty.workspace = true
 project.workspace = true
+prompt_store.workspace = true
 regex.workspace = true
 rust-embed.workspace = true
 schemars.workspace = true