Bug Description

Using the hermes tools command and completing the setup makes the MCP tools disappear from the platforms in the config.yaml. Because of this, none of the MCP tools are readable by Hermes and they have to be added manually.

Also, MCPs are not available unless you add them in the platform_toolsets entry in the config.yaml file.

Steps to Reproduce

1. Run hermes tools command.
2. Make global or platform (CLI, Telegram, etc.) changes.
3. Confirm changes; config.yaml is saved.

Expected Behavior

1. Run hermes tools command.
2. Make global or platform (CLI, Telegram, etc.) changes.
3. Confirm changes and save config.
4. MCPs are discoverable, even if they are not listed in platform_toolsets.

Actual Behavior

1. Run hermes tools command.
2. Make global or platform (CLI, Telegram, etc.) changes.
3. Confirm changes; MCPs are removed from the platform_toolsets entry in the config.yaml.
4. MCPs are not available for the agent (this can be confirmed by running the command /toolsets in the CLI.

Affected Component

Configuration (config.yaml, .env, hermes setup)

Messaging Platform (if gateway-related)

No response

Operating System

Ubuntu 24.04

Python Version

3.11.15

Hermes Version

0.2.0

Relevant Logs / Traceback

Root Cause Analysis (optional)

No response

Proposed Fix (optional)

No response

Are you willing to submit a PR for this?

• I'd like to fix this myself and submit a PR