The harness instructs them to behave this way. Also this approach saves tokens. The scripts allow to edit files in bulk, and most of the session cost is in cache reads (e.g. for 300K context each command costs the same as 30K input tokens).

Why would you use a constrained edit tool when you are also allowed to use the complete power of python?

This is an instruction by the harness. It re-injects the prompt every other message, so that's why it "forgets" to use the Edit tool.

this is intentional, afaik agents do better with python and alike than the harness tooling.

I use AST replacers, much more reliable.

Sounds like you don't have enough experience with coding agents. Deterministic scripts must always be preferred instead of LLM tool calls. In fact, you should instruct your agents to write code to execute instead of letting them call tools.