PR #24923: fix(clarify): treat timeout as refusal instead of implicit consent

• Repository: NousResearch/hermes-agent
• Author: liuhao1024
• State: open | merged: False
• Link: https://github.com/NousResearch/hermes-agent/pull/24923

Description (problem / solution / changelog)

Summary

When the clarify tool times out (user does not respond within the configured window), the CLI callback currently returns:

"Use your best judgement to make the choice and proceed."

The LLM interprets this as permission to execute whatever action it was asking about — including destructive operations like rm -rf .git. This is a security/safety failure: silence is not consent.

Root Cause

In hermes_cli/callbacks.py, the clarify_callback function handles timeout by returning a message that explicitly tells the agent to proceed:

return (
    "The user did not provide a response within the time limit. "
    "Use your best judgement to make the choice and proceed."
)

This message is then passed to the LLM as the user's "response" to the clarify question. For permission-seeking questions ("May I delete .git?"), the LLM reads this as approval.

Fix

1. hermes_cli/callbacks.py: Changed the timeout return message to explicitly refuse — "Treat this as a refusal — do NOT proceed with any pending destructive or irreversible action."

2. tools/clarify_tool.py: Added timeout-refusal guidance to the tool description so the LLM understands the expected behavior before it even calls the tool.

3. Regression test: Added test_timeout_refusal_response_passed_through to verify refusal messages are not overwritten by permissive language.

Testing

• All 21 tests in tests/tools/test_clarify_tool.py pass (including the new regression test)
• All 14 tests in tests/tools/test_clarify_gateway.py pass

Notes

• The oneshot callback (hermes_cli/oneshot.py) intentionally uses permissive language for non-interactive hermes run mode — this is correct since oneshot has no user present.
• The gateway does not pass a clarify_callback to AIAgent, so the clarify tool returns an error in gateway mode. This is a separate issue — the gateway should have its own clarify handling with proper timeout refusal behavior.
• The TUI callback (tui_gateway/server.py) uses _block which waits indefinitely for the TUI response — no timeout handling needed there.

Fixes [Bug]: Agent assumes consent without it was given #24912

Changed files

• hermes_cli/callbacks.py (modified, +4/-2)
• tests/tools/test_clarify_tool.py (modified, +20/-0)
• tools/clarify_tool.py (modified, +2/-0)