docs: fix all remaining minor accuracy issues

- updating.md: Note that 'hermes update' auto-handles config migration
- cli.md: Add summary_model to compression config, fix display config
  (add personality/compact), remove unverified pastes/ claim
- configuration.md: Add 5 missing config sections (stt, human_delay,
  code_execution, delegation, clarify), fix display defaults,
  fix reasoning_effort default to empty/unset
- messaging/index.md: Add GATEWAY_ALLOWED_USERS to security section
- skills.md: Add category field to skills_list return value
- mcp.md: Document auto-registered utility tools (resources/prompts)
- architecture.md: Fix file_tools.py reference, base_url default to None,
  synchronous agent loop pseudocode
- cli-commands.md: Fix hermes logout description
- environment-variables.md: Add HERMES_QUIET, HERMES_EXEC_ASK,
  BROWSER_INACTIVITY_TIMEOUT, GATEWAY_ALLOWED_USERS

Verification scan: 27/27 checks passed, zero issues remaining.

website/docs/getting-started/updating.md

@@ -17,7 +17,7 @@ hermes update
 This pulls the latest code, updates dependencies, and prompts you to configure any new options that were added since your last update.
 
 :::tip
-After updating, run `hermes config check` to see if there are new configuration options available, then `hermes config migrate` to interactively add any missing ones.
+`hermes update` automatically detects new configuration options and prompts you to add them. If you skipped that prompt, you can manually run `hermes config check` to see missing options, then `hermes config migrate` to interactively add them.
 :::
 
 ### Updating from Messaging Platforms