Customize sessions in self-hosted environments

 
 The runner gives each session its own config directory, seeded from an in-memory snapshot of the host's `~/.claude/` that the runner captures once at startup: `settings.json`, `CLAUDE.md`, hooks, agents, commands, and skills in your runner image apply to every session as the user-level baseline. Because the snapshot is taken at startup, config changes on a running host take effect only after a runner restart. Set `SELF_HOSTED_RUNNER_HOST_CONFIG_DIR` to seed from a different path, or point it at an empty directory to disable seeding.
 
-Repository-committed `.claude/settings.json` layers on top as project settings. Sessions also read [`managed-settings.json`](/docs/en/settings#settings-files) from the standard system path in your runner image, but the managed tier uses one source at a time, and [server-managed settings](/docs/en/server-managed-settings) are checked first: if your organization delivers any server-managed keys, sessions ignore the runner image's managed file, except that `env` blocks merge per key across managed sources. See [settings precedence](/docs/en/settings#settings-precedence).
+Repository-committed `.claude/settings.json` layers on top as project settings. Sessions also read [`managed-settings.json`](/docs/en/settings#where-settings-live) from the standard system path in your runner image, but the managed tier uses one source at a time, and [server-managed settings](/docs/en/server-managed-settings) are checked first: if your organization delivers any server-managed keys, sessions ignore the runner image's managed file, except that `env` blocks merge per key across managed sources. See [settings precedence](/docs/en/settings#settings-precedence).
 
 When Anthropic's control plane supplies a session with [Claude Code hooks](/docs/en/hooks), the runner installs them alongside, not over, your own configuration. Requires Claude Code v2.1.229 or later.
 
 * **Where they land**: the runner writes each supplied hook script to a reserved `hooks/.ccr-launcher/` subdirectory of the session's config directory and registers the scripts in a separate settings file it passes to the session with `--settings`, leaving the seeded `settings.json` and your own scripts at `hooks/<name>` untouched. The runner recreates the reserved subdirectory for each session and doesn't seed host content at `~/.claude/hooks/.ccr-launcher/` into sessions.
 * **Who authors them**: the control plane populates the scripts from fixed constants in its own deployment, never from per-session or third-party input.
-* **What still governs them**: hooks delivered through `--settings` enter the ordinary merged hook configuration, not the managed tier, so your managed settings still apply. `disableAllHooks` disables them, and they are not among the categories [`allowManagedHooksOnly`](/docs/en/settings#hook-configuration) keeps loaded.
+* **What still governs them**: hooks delivered through `--settings` enter the ordinary merged hook configuration, not the managed tier, so your managed settings still apply. `disableAllHooks` disables them, and they are not among the categories [`allowManagedHooksOnly`](/docs/en/settings-reference#allowmanagedhooksonly) keeps loaded.
 
 ### Repository-committed permission rules