app-server: use permission ids and runtime workspace roots (#22611)

## Why

This PR builds on [#22610](https://github.com/openai/codex/pull/22610)
and is the app-server side of the migration from mutable per-turn
`SandboxPolicy` replacement toward selecting immutable permission
profiles by id plus mutable runtime workspace roots.

Once permission profiles can carry their own immutable
`workspace_roots`, app-server no longer needs to mutate the selected
`PermissionProfile` just to represent thread-specific filesystem
context. The mutable part now lives on the thread as explicit
`runtimeWorkspaceRoots`, while `:workspace_roots` remains symbolic until
the sandbox is realized for a turn.

## What Changed

- Replaced the v2 permission-selection wrapper surface with plain
profile ids for `thread/start`, `thread/resume`, `thread/fork`, and
`turn/start`.
- Removed the API surface for profile modifications
(`PermissionProfileSelectionParams`,
`PermissionProfileModificationParams`,
`ActivePermissionProfileModification`).
- Added experimental `runtimeWorkspaceRoots` fields to the thread
lifecycle and turn-start APIs.
- Threaded runtime workspace roots through core session/thread
snapshots, turn overrides, app-server request handling, and command
execution permission resolution.
- Kept session permission state symbolic so later runtime root updates
and cwd-only implicit-root retargeting rebind `:workspace_roots`
correctly.
- Updated the embedded clients just enough to send and restore the new
thread state.
- Refreshed the generated schema/TypeScript artifacts and the app-server
README to match the new contract.

## Verification

Targeted coverage for this layer lives in:

- `codex-rs/app-server-protocol/src/protocol/v2/tests.rs`
- `codex-rs/app-server/tests/suite/v2/thread_start.rs`
- `codex-rs/app-server/tests/suite/v2/thread_resume.rs`
- `codex-rs/app-server/tests/suite/v2/turn_start.rs`
- `codex-rs/core/src/session/tests.rs`

The key regression checks exercise that:

- `runtimeWorkspaceRoots` resolve against the effective cwd on thread
start.
- Profile-declared workspace roots are excluded from the runtime
workspace roots returned by app-server.
- A turn-level runtime workspace-root update persists onto the thread
and is returned by `thread/resume`.
- A named permission profile selected on one turn remains symbolic so a
later runtime-root-only turn update changes the actual sandbox writes.
- A cwd-only turn update retargets the implicit runtime cwd root while
preserving additional runtime roots.
- The protocol fixtures and generated client artifacts stay in sync with
the string-based permission selection contract.











---
[//]: # (BEGIN SAPLING FOOTER)
Stack created with [Sapling](https://sapling-scm.com). Best reviewed
with [ReviewStack](https://reviewstack.dev/openai/codex/pull/22611).
* #22612
* __->__ #22611

codex-rs/app-server-protocol/schema/json/codex_app_server_protocol.schemas.json

@@ -11739,31 +11739,6 @@
           }
         ]
       },
-      "PermissionProfileModificationParams": {
-        "oneOf": [
-          {
-            "description": "Additional concrete directory that should be writable.",
-            "properties": {
-              "path": {
-                "$ref": "#/definitions/v2/AbsolutePathBuf"
-              },
-              "type": {
-                "enum": [
-                  "additionalWritableRoot"
-                ],
-                "title": "AdditionalWritableRootPermissionProfileModificationParamsType",
-                "type": "string"
-              }
-            },
-            "required": [
-              "path",
-              "type"
-            ],
-            "title": "AdditionalWritableRootPermissionProfileModificationParams",
-            "type": "object"
-          }
-        ]
-      },
       "PermissionProfileNetworkPermissions": {
         "properties": {
           "enabled": {
@@ -11775,40 +11750,6 @@
         ],
         "type": "object"
       },
-      "PermissionProfileSelectionParams": {
-        "oneOf": [
-          {
-            "description": "Select a named built-in or user-defined profile and optionally apply bounded modifications that Codex knows how to validate.",
-            "properties": {
-              "id": {
-                "type": "string"
-              },
-              "modifications": {
-                "items": {
-                  "$ref": "#/definitions/v2/PermissionProfileModificationParams"
-                },
-                "type": [
-                  "array",
-                  "null"
-                ]
-              },
-              "type": {
-                "enum": [
-                  "profile"
-                ],
-                "title": "ProfilePermissionProfileSelectionParamsType",
-                "type": "string"
-              }
-            },
-            "required": [
-              "id",
-              "type"
-            ],
-            "title": "ProfilePermissionProfileSelectionParams",
-            "type": "object"
-          }
-        ]
-      },
       "Personality": {
         "enum": [
           "none",