Summary

cli.py now stores/reads prefill config under agent.prefill_messages_file, but the canonical config schema and the gateway/cron loaders still use the root-level prefill_messages_file key. As a result, a valid ~/.hermes/config.yaml entry can work in gateway/cron paths while being silently ignored in the standalone CLI.

Affected code

• cli.py:249-253 — CLI defaults place prefill_messages_file under agent
• cli.py:1735-1738 — runtime only reads CLI_CONFIG["agent"].get("prefill_messages_file", "")
• hermes_cli/config.py:610-614 — canonical config schema still exposes root-level prefill_messages_file
• gateway/run.py:1071-1085 — gateway still reads root-level prefill_messages_file
• cron/scheduler.py:658-660 — cron still reads root-level prefill_messages_file

Why this is a bug

The same config key is interpreted differently across entrypoints:

• gateway/cron accept prefill_messages_file at the config root
• CLI ignores that same root-level key and only checks agent.prefill_messages_file

That means a user can have a valid config according to the schema/docs and still lose their few-shot prefill behavior in the CLI with no error.

Minimal reproduction

import tempfile, pathlib, importlib, json, os, sys
sys.path.insert(0, "/Users/genie/.hermes/hermes-agent")

with tempfile.TemporaryDirectory() as td:
    home = pathlib.Path(td)
    (home / "config.yaml").write_text("prefill_messages_file: prefill.json\n", encoding="utf-8")
    os.environ["HERMES_HOME"] = str(home)
    sys.modules.pop("cli", None)
    import cli
    cli._hermes_home = home
    cfg = cli.load_cli_config()
    print(cfg.get("prefill_messages_file"))          # "prefill.json"
    print(cfg.get("agent", {}).get("prefill_messages_file"))  # ""

Observed in this repo:

• root-level value survives config load
• CLI runtime lookup is empty because it only checks cfg["agent"]["prefill_messages_file"]

Expected behavior

All Hermes entrypoints should accept the same config location for prefill messages, or the CLI should preserve a backward-compatible fallback from the root-level key.

Actual behavior

A root-level prefill_messages_file works in gateway/cron code paths but is silently ignored by the CLI.

Suggested investigation

Choose one canonical location and normalize consistently during config loading. If agent.prefill_messages_file is the new home, load_cli_config() should still map the legacy root-level key into agent.prefill_messages_file so existing configs keep working.