fix(desktop): keep composer usable during reconnect (#45488)

* feat(cli): add --safe-mode troubleshooting flag

Inspired by Claude Code v2.1.169 (June 2026): run Hermes with all
customizations disabled to isolate setup problems from product bugs.

--safe-mode implies --ignore-user-config and --ignore-rules, and
additionally skips plugin discovery (hermes_cli/plugins.py) and MCP
server loading (tools/mcp_tool.py) via the internal HERMES_SAFE_MODE
env bridge.

* fix(desktop): keep composer usable during reconnect

website/docs/reference/environment-variables.md

@@ -595,6 +595,7 @@ Advanced per-platform knobs for throttling the outbound message batcher. Most us
 | `HERMES_ACCEPT_HOOKS` | Auto-approve any unseen shell hooks declared in `config.yaml` without a TTY prompt. Equivalent to `--accept-hooks` or `hooks_auto_accept: true`. |
 | `HERMES_IGNORE_USER_CONFIG` | Skip `~/.hermes/config.yaml` and use built-in defaults (credentials in `.env` still load). Equivalent to `--ignore-user-config`. |
 | `HERMES_IGNORE_RULES` | Skip auto-injection of `AGENTS.md`, `SOUL.md`, `.cursorrules`, memory, and preloaded skills. Equivalent to `--ignore-rules`. |
+| `HERMES_SAFE_MODE` | Troubleshooting mode: disable ALL customizations — skips plugin discovery and MCP server loading. Set automatically by `--safe-mode` (which also sets the two flags above). |
 | `HERMES_MD_NAMES` | Comma-separated list of rules-file names to auto-inject (default: `AGENTS.md,CLAUDE.md,.cursorrules,SOUL.md`). |
 | `HERMES_TOOL_PROGRESS` | Deprecated compatibility variable for tool progress display. Prefer `display.tool_progress` in `config.yaml`. |
 | `HERMES_TOOL_PROGRESS_MODE` | Deprecated compatibility variable for tool progress mode. Prefer `display.tool_progress` in `config.yaml`. |