docs(config): document unmanaged TOML table retention

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

README.md

@@ -218,7 +218,7 @@ backed up and retained with a warning. Backups are stored under `backups/<timest
 Codex skill backups use `.agents/.ai-config-skill-backups/` instead, so Codex does not discover backup copies as skills.
 Existing `.agents/skills/backups/` content is moved there on the next install, update, or uninstall.
 Codex `config.toml` synchronization merges setup-owned keys while retaining other root keys, extra fields in managed
-tables, plugin and marketplace tables, and unowned array tables. Other standalone tables may be dropped; the previous
+tables, plugin and marketplace tables, other unmanaged tables, and unowned array tables. The previous
 file is backed up when content changes. Claude `settings.json` synchronization retains unrelated settings and hooks.
 Dry runs still rebuild `generated/`, but do not modify installation destinations.
 

docs/configuration.md

@@ -37,4 +37,4 @@ The agent chooses the smallest sufficient checks based on behavior, affected cal
 
 Delegation and long-running state use the shared orchestration rule, loaded on demand as a Codex rule or Claude skill. The coordinator owns decisions and routes concise evidence-based handoffs. Review and execution verification have separate responsibilities; see [Agents](agents.md).
 
-Rebuild packages after changes to shared definitions or adapters. Generated defaults reach a user's configuration only through installation or update. Updates merge Codex's setup-owned root keys and table fields while retaining other root keys, extra fields in managed tables, plugin and marketplace tables, and unowned array tables. Other standalone tables may be dropped. Claude settings retain unrelated keys and hooks. See [the README](../README.md) for overwrite and backup behavior.
+Rebuild packages after changes to shared definitions or adapters. Generated defaults reach a user's configuration only through installation or update. Updates merge Codex's setup-owned root keys and table fields while retaining other root keys, extra fields in managed tables, plugin and marketplace tables, other unmanaged tables such as `mcp_servers` and `model_providers`, and unowned array tables. Claude settings retain unrelated keys and hooks. See [the README](../README.md) for overwrite and backup behavior.

docs/plugins.md

@@ -10,7 +10,7 @@ Selecting Context7 with MCPorter registers the server in MCPorter. Selecting Con
 
 `update.ps1`/`update.sh` lets you revise the saved extension selection. Checking an extension installs it if missing or updates it if owned; existing foreign installations are preserved. Deselection removes only extensions that this setup installed and recorded as owned. Pre-existing or manually installed plugins and skills are retained. Extensions removed from the manifest are also removed when recorded as owned; unrelated installations are retained. Update refuses to run if any selected destination lacks an installation manifest (`Not installed, use the install script.`).
 
-Codex's local `plugins` and `marketplaces` tables survive configuration synchronization, along with other root keys, extra fields in managed tables, and unowned array tables. Other standalone tables may be dropped; changed files are backed up. Cached plugin files alone are not treated as proof of installation: selection uses the client CLI's installed list. If an older update removed the registrations, inspect the backed-up `config.toml` under `~/.codex/backups/` and reselect the affected plugins on the next update.
+Codex's local `plugins` and `marketplaces` tables survive configuration synchronization, along with other root keys, extra fields in managed tables, other unmanaged tables, and unowned array tables; changed files are backed up. Cached plugin files alone are not treated as proof of installation: selection uses the client CLI's installed list. If an older update removed the registrations, inspect the backed-up `config.toml` under `~/.codex/backups/` and reselect the affected plugins on the next update.
 
 Codex receives Caveman through its native plugin adapter. Humanizer, Impeccable, and Anthropic Frontend Design are downloaded as skill payloads from the GitHub sources in the manifest, without running upstream installers. All three appear in the extension selector for Codex. Ownership is recorded in `~/.my-ai-configuration/extensions.json`. Skill files are tracked by hash; modified or foreign files are retained with a warning. Existing installations from before ownership tracking are not automatically adopted.