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/src/request_processors/thread_processor.rs

@@ -59,6 +59,25 @@ fn collect_resume_override_mismatches(
             ));
         }
     }
+    if let Some(requested_runtime_workspace_roots) = request.runtime_workspace_roots.as_ref() {
+        let base_cwd = request
+            .cwd
+            .as_deref()
+            .map(|cwd| {
+                AbsolutePathBuf::resolve_path_against_base(cwd, config_snapshot.cwd.as_path())
+            })
+            .unwrap_or_else(|| config_snapshot.cwd.clone());
+        let requested_runtime_workspace_roots = requested_runtime_workspace_roots
+            .iter()
+            .map(|path| AbsolutePathBuf::resolve_path_against_base(path, base_cwd.as_path()))
+            .collect::<Vec<_>>();
+        if requested_runtime_workspace_roots != config_snapshot.workspace_roots {
+            mismatch_details.push(format!(
+                "runtime_workspace_roots requested={requested_runtime_workspace_roots:?} active={:?}",
+                config_snapshot.workspace_roots
+            ));
+        }
+    }
     if let Some(requested_approval) = request.approval_policy.as_ref() {
         let active_approval: AskForApproval = config_snapshot.approval_policy.into();
         if requested_approval != &active_approval {
@@ -804,6 +823,7 @@ impl ThreadRequestProcessor {
             model_provider,
             service_tier,
             cwd,
+            runtime_workspace_roots,
             approval_policy,
             approvals_reviewer,
             sandbox,
@@ -837,6 +857,7 @@ impl ThreadRequestProcessor {
             model_provider,
             service_tier,
             cwd,
+            runtime_workspace_roots,
             approval_policy,
             approvals_reviewer,
             sandbox,
@@ -1173,6 +1194,7 @@ impl ThreadRequestProcessor {
             model_provider: config_snapshot.model_provider_id,
             service_tier: config_snapshot.service_tier,
             cwd: config_snapshot.cwd,
+            runtime_workspace_roots: config_snapshot.workspace_roots,
             instruction_sources,
             approval_policy: config_snapshot.approval_policy.into(),
             approvals_reviewer: config_snapshot.approvals_reviewer.into(),
@@ -1214,6 +1236,7 @@ impl ThreadRequestProcessor {
         model_provider: Option<String>,
         service_tier: Option<Option<String>>,
         cwd: Option<String>,
+        runtime_workspace_roots: Option<Vec<PathBuf>>,
         approval_policy: Option<codex_app_server_protocol::AskForApproval>,
         approvals_reviewer: Option<codex_app_server_protocol::ApprovalsReviewer>,
         sandbox: Option<SandboxMode>,
@@ -1227,6 +1250,7 @@ impl ThreadRequestProcessor {
             model_provider,
             service_tier,
             cwd: cwd.map(PathBuf::from),
+            workspace_roots: runtime_workspace_roots,
             approval_policy: approval_policy
                 .map(codex_app_server_protocol::AskForApproval::to_core),
             approvals_reviewer: approvals_reviewer
@@ -2351,6 +2375,7 @@ impl ThreadRequestProcessor {
             model_provider,
             service_tier,
             cwd,
+            runtime_workspace_roots,
             approval_policy,
             approvals_reviewer,
             sandbox,
@@ -2386,6 +2411,7 @@ impl ThreadRequestProcessor {
             model_provider,
             service_tier,
             cwd,
+            runtime_workspace_roots,
             approval_policy,
             approvals_reviewer,
             sandbox,
@@ -2523,6 +2549,7 @@ impl ThreadRequestProcessor {
                     model_provider: session_configured.model_provider_id,
                     service_tier: session_configured.service_tier,
                     cwd: session_configured.cwd,
+                    runtime_workspace_roots: config_snapshot.workspace_roots,
                     instruction_sources,
                     approval_policy: session_configured.approval_policy.into(),
                     approvals_reviewer: session_configured.approvals_reviewer.into(),
@@ -2987,6 +3014,7 @@ impl ThreadRequestProcessor {
             model_provider,
             service_tier,
             cwd,
+            runtime_workspace_roots,
             approval_policy,
             approvals_reviewer,
             sandbox,
@@ -3052,6 +3080,7 @@ impl ThreadRequestProcessor {
             model_provider,
             service_tier,
             cwd,
+            runtime_workspace_roots,
             approval_policy,
             approvals_reviewer,
             sandbox,
@@ -3181,6 +3210,7 @@ impl ThreadRequestProcessor {
             model_provider: session_configured.model_provider_id,
             service_tier: session_configured.service_tier,
             cwd: session_configured.cwd,
+            runtime_workspace_roots: config_snapshot.workspace_roots,
             instruction_sources,
             approval_policy: session_configured.approval_policy.into(),
             approvals_reviewer: session_configured.approvals_reviewer.into(),