Config writes destroy existing Claude Code, Codex, and Gemini CLI settings

[datasciencemonkey]

Problem

When running coding-gateway configure or launching a tool, the CLI fully overwrites the config files for all three supported tools:

• Claude Code (~/.claude/settings.json): Overwrites the entire file with just apiKeyHelper + env. This destroys mcpServers, permissions, hooks, allow rules, enabledPlugins, and all other user settings.
• Codex (~/.codex/config.toml): Replaces the entire file with a single Databricks profile, destroying any user-defined profiles or model providers.
• Gemini CLI (~/.gemini/.env): Replaces the entire file with 4 gateway variables. The token refresh thread also re-overwrites the file every 30 minutes.

This happens on every launch, not just during explicit configuration.

Impact

• Users lose MCP server configurations, permission rules, hooks, plugin settings, and custom env vars
• The backup mechanism only captures the config from the very first run and is never updated
• Users who have customized their Claude Code setup will have everything silently destroyed

Expected Behavior

The tool should read-merge-write: read existing config, deep-merge only the keys it manages, and write back — preserving everything else. On logout, it should surgically remove only its managed keys.

Acceptance Criteria

• Claude settings.json merge: only apiKeyHelper and gateway env vars are written; all other keys preserved
• Gemini .env merge: only 4 gateway vars are updated; other env vars preserved
• Logout surgically removes gateway-managed keys instead of restoring stale backups
• Unit tests verify merge/unmerge round-trips preserve user settings
• Tested against a real Claude Code settings file with MCP servers, hooks, plugins