chore: include User layer in ConfigLayerStack even if config.toml is empty (#8456)

This is necessary so that `$CODEX_HOME/skills` and `$CODEX_HOME/rules`
still get loaded even if `$CODEX_HOME/config.toml` does not exist. See
#8453.

For now, it is possible to omit this layer when creating a dummy
`ConfigLayerStack` in a test. We can revisit that later, if it turns out
to be the right thing to do.

codex-rs/app-server-protocol/src/protocol/v2.rs

@@ -237,6 +237,8 @@ pub enum ConfigLayerSource {
     #[serde(rename_all = "camelCase")]
     #[ts(rename_all = "camelCase")]
     User {
+        /// This is the path to the user's config.toml file, though it is not
+        /// guaranteed to exist.
         file: AbsolutePathBuf,
     },