Add runtime extra skill roots API (#24977)

## Summary
- Add v2 `skills/extraRoots/set` to replace app-server process-local
standalone skill roots. The setting is not persisted, accepts missing
roots, and `extraRoots: []` clears the runtime set.
- Wire runtime roots into core skill discovery for `skills/list` and
turn loads, clear skill caches on set, and register the roots with the
skills watcher so later filesystem changes emit `skills/changed`.
- Update app-server docs, generated JSON/TypeScript schemas, and
coverage for serialization, missing roots, empty clears, and restart
behavior.

## Testing
- `cargo test -p codex-app-server-protocol`
- `cargo test -p codex-core-skills`
- `cargo test -p codex-app-server
skills_extra_roots_set_updates_process_runtime_roots`
- `just fix -p codex-app-server-protocol`
- `just fix -p codex-core-skills`
- `just fix -p codex-app-server`

codex-rs/app-server-protocol/schema/json/ClientRequest.json

@@ -2988,6 +2988,20 @@
       ],
       "type": "object"
     },
+    "SkillsExtraRootsSetParams": {
+      "properties": {
+        "extraRoots": {
+          "items": {
+            "$ref": "#/definitions/AbsolutePathBuf"
+          },
+          "type": "array"
+        }
+      },
+      "required": [
+        "extraRoots"
+      ],
+      "type": "object"
+    },
     "SkillsListParams": {
       "properties": {
         "cwds": {
@@ -4783,6 +4797,30 @@
       "title": "Skills/listRequest",
       "type": "object"
     },
+    {
+      "properties": {
+        "id": {
+          "$ref": "#/definitions/RequestId"
+        },
+        "method": {
+          "enum": [
+            "skills/extraRoots/set"
+          ],
+          "title": "Skills/extraRoots/setRequestMethod",
+          "type": "string"
+        },
+        "params": {
+          "$ref": "#/definitions/SkillsExtraRootsSetParams"
+        }
+      },
+      "required": [
+        "id",
+        "method",
+        "params"
+      ],
+      "title": "Skills/extraRoots/setRequest",
+      "type": "object"
+    },
     {
       "properties": {
         "id": {