Remove skills list extra roots (#21485)

## Summary
- Remove `perCwdExtraUserRoots` / `SkillsListExtraRootsForCwd` from the
`skills/list` app-server API.
- Drop Rust app-server and `codex-core-skills` extra-root plumbing so
skill scans are keyed by the normal cwd/user/plugin roots only.
- Regenerate app-server schemas and update docs/tests that only existed
for the removed extra-roots behavior.

## Validation
- `just write-app-server-schema`
- `just fmt`
- `cargo test -p codex-app-server-protocol`
- `cargo test -p codex-core-skills`
- `just fix -p codex-app-server-protocol`
- `just fix -p codex-core-skills`
- `just fix -p codex-app-server`
- `just fix -p codex-tui`

## Notes
- `cargo test -p codex-app-server --test all skills_list` ran the edited
skills-list cases, but the full filtered run ended on existing
`skills_changed_notification_is_emitted_after_skill_change` timeout
after a websocket `401`.
- `cargo test -p codex-tui --lib` compiled the changed TUI callers, then
failed two unrelated status permission tests because local
`/etc/codex/requirements.toml` forbids `DangerFullAccess`.
- Source-truth check found the OpenAI monorepo still has
generated/app-server-kit mirror references to the removed field; those
should be cleaned up when generated app-server types are synced or in a
companion OpenAI cleanup.

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

@@ -1656,7 +1656,6 @@ mod tests {
             params: v2::SkillsListParams {
                 cwds: Vec::new(),
                 force_reload: false,
-                per_cwd_extra_user_roots: None,
             },
         };
         assert_eq!(

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

@@ -15,7 +15,7 @@ use serde::Serialize;
 use std::path::PathBuf;
 use ts_rs::TS;
 
-#[derive(Serialize, Deserialize, Debug, Clone, PartialEq, JsonSchema, TS)]
+#[derive(Serialize, Deserialize, Debug, Clone, Default, PartialEq, JsonSchema, TS)]
 #[serde(rename_all = "camelCase")]
 #[ts(export_to = "v2/")]
 pub struct SkillsListParams {
@@ -26,19 +26,6 @@ pub struct SkillsListParams {
     /// When true, bypass the skills cache and re-scan skills from disk.
     #[serde(default, skip_serializing_if = "std::ops::Not::not")]
     pub force_reload: bool,
-
-    /// Optional per-cwd extra roots to scan as user-scoped skills.
-    #[serde(default)]
-    #[ts(optional = nullable)]
-    pub per_cwd_extra_user_roots: Option<Vec<SkillsListExtraRootsForCwd>>,
-}
-
-#[derive(Serialize, Deserialize, Debug, Clone, PartialEq, JsonSchema, TS)]
-#[serde(rename_all = "camelCase")]
-#[ts(export_to = "v2/")]
-pub struct SkillsListExtraRootsForCwd {
-    pub cwd: PathBuf,
-    pub extra_user_roots: Vec<PathBuf>,
 }
 
 #[derive(Serialize, Deserialize, Debug, Clone, PartialEq, JsonSchema, TS)]

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

@@ -2508,33 +2508,20 @@ fn skills_list_params_serialization_uses_force_reload() {
         serde_json::to_value(SkillsListParams {
             cwds: Vec::new(),
             force_reload: false,
-            per_cwd_extra_user_roots: None,
         })
         .unwrap(),
-        json!({
-            "perCwdExtraUserRoots": null,
-        }),
+        json!({}),
     );
 
     assert_eq!(
         serde_json::to_value(SkillsListParams {
             cwds: vec![PathBuf::from("/repo")],
             force_reload: true,
-            per_cwd_extra_user_roots: Some(vec![SkillsListExtraRootsForCwd {
-                cwd: PathBuf::from("/repo"),
-                extra_user_roots: vec![PathBuf::from("/shared/skills"), PathBuf::from("/tmp/x")],
-            }]),
         })
         .unwrap(),
         json!({
             "cwds": ["/repo"],
             "forceReload": true,
-            "perCwdExtraUserRoots": [
-                {
-                    "cwd": "/repo",
-                    "extraUserRoots": ["/shared/skills", "/tmp/x"],
-                }
-            ],
         }),
     );
 }