[exec] Clean up apply-patch tests (#2648)

## Summary
These tests were getting a bit unwieldy, and they're starting to become
load-bearing. Let's clean them up, and get them working solidly so we
can easily expand this harness with new tests.

## Test Plan
- [x] Tests continue to pass

codex-rs/exec/tests/fixtures/apply_patch_freeform_final.txt

@@ -0,0 +1,4 @@
+class BaseClass:
+  def method():
+
+    return True