Per-round LLM log files live under <datalog_dir>/llm/ where
<datalog_dir> is the per-project directory resolved by
DatalogWriter::resolve_log_dir (typically
~/.atomcode/datalog/<project-slug>/). The caller is responsible for
passing in the resolved dir — see runner.rs. This keeps the JSONL dump
in lockstep with the markdown writer’s [datalog].dir config; the prior
hard-coded <working_dir>/datalog/llm/ would silently ignore the user’s
dir override.
Log the LLM response by merging it into the request file identified by
pending_request. If pending_request is None (no prior request, or
request write failed), writes a standalone *_orphan_response.json
marked with a warning. Also appends a one-line summary to calls.log.