## Description
This PR makes new threads with `history_mode = "paginated"` persist
`ItemCompleted(item: <turn_item>)` in their rollout JSONL file.
Legacy threads keep persisting the existing legacy events. Because the
format is selected per thread, a rollout is either legacy or paginated;
we do not need to support mixed rollouts containing both
representations.
This PR depends on [#31473](https://github.com/openai/codex/pull/31473).
## Why
Paginated thread history needs stable turn/item IDs and completed item
snapshots so the later SQLite projector can materialize appended rollout
JSONL without rebuilding the whole thread.
Keeping the legacy persistence policy unchanged avoids changing
historical rollouts or the readers that still consume them.
## What changed
- Made rollout filtering history-mode aware. Paginated threads keep
completed canonical `ItemCompleted` events and drop their redundant
legacy projections; legacy threads keep the existing event set.
- Made forks inherit the source thread history mode, so copied legacy
history is never filtered as paginated.
- Made paginated threads assign IDs to locally-created response items
even when `Feature::ItemIds` is off, and reject streamed output items
that arrive without server IDs.
- Updated legacy turn replay, rollout list/search, and SQLite metadata
extraction to understand completed canonical user-message items.
## Summary
A cold-resumed subagent kept its durable thread ID but could receive a
new session ID, splitting one agent tree across multiple sessions after
a restart.
Persist the root session ID in every rollout `SessionMeta`, carry it
through thread creation, and restore it before initializing the resumed
`Session` and `AgentControl`.
## Behavior
For a nested agent tree:
```text
root session R
parent thread P
child thread C
```
The child rollout stores:
```text
session_id: R
parent_thread_id: P
id: C
```
After a cold resume, the child still belongs to root session `R` while
its immediate parent remains `P`. The integration coverage uses distinct
values for all three IDs so it catches restoring the session from
`parent_thread_id`.
## Legacy rollouts
Previous rollouts have `id` but no `session_id`. `SessionMetaLine`
deserialization treats a missing `session_id` as `id`, keeping those
files readable, listable, and resumable. When a legacy subagent is
resumed through its root, that synthesized child ID no longer overrides
the inherited root-scoped `AgentControl`. New rollouts always persist
the explicit root session ID.
## Why
The v2 app-server permission profile fields are experimental, but the
previous migration kept a legacy object payload for profile selection.
That made clients aware of server-owned `activePermissionProfile`
metadata such as `extends`, and it kept a
`legacy_additional_writable_roots` path even though
`runtimeWorkspaceRoots` now owns runtime workspace-root selection.
This PR makes the client contract match the intended model: clients
select a permission profile by id, and the server resolves and reports
active profile provenance in response payloads.
Follow-up to #22611.
## What Changed
- Changed `thread/start`, `thread/resume`, `thread/fork`, and
`turn/start` permission profile selection to plain profile id strings.
- Changed `command/exec.permissionProfile` to a plain profile id string
for the same client/server ownership split.
- Removed `PermissionProfileSelectionParams` and the legacy `{ type:
"profile", modifications: [...] }` compatibility deserializer.
- Updated app-server, TUI, and `codex exec` call sites to send only ids,
while keeping `activePermissionProfile` as server response metadata.
- Updated app-server docs and schema fixtures for the revised
`command/exec.permissionProfile` shape.
## Verification
- `cargo test -p codex-app-server-protocol`
- `RUST_MIN_STACK=8388608 cargo test -p codex-app-server`
- `cargo test -p codex-exec`
- `RUST_MIN_STACK=8388608 cargo test -p codex-tui`
---
[//]: # (BEGIN SAPLING FOOTER)
Stack created with [Sapling](https://sapling-scm.com). Best reviewed
with [ReviewStack](https://reviewstack.dev/openai/codex/pull/23360).
* #23368
* __->__ #23360
## 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
## Why
The app-server request path had grown around a large
`CodexMessageProcessor` plus separate API wrapper/helper modules. That
made the dependency graph hard to see and forced unrelated request
families to share broad processor state.
This PR makes the split mechanical and command-prefix oriented so
request families own only the dependencies they use.
## What changed
- Replaced `CodexMessageProcessor` with command-prefix request
processors under `app-server/src/request_processors/`.
- Removed the old config, device-key, external-agent-config, and fs API
wrapper files by moving their API handling into processors.
- Split apps, plugins, marketplace, catalog, account, MCP, command exec,
fs, git, feedback, thread, turn, thread goals, and Windows sandbox
handling into dedicated processors.
- Kept shared lifecycle, summary conversion, token usage replay, and
shared error mapping only where multiple processors use them; single-use
helpers were inlined into their owning processor.
- Removed the fallback processor path and moved processor tests to
`_tests` files.
## Validation
- `cargo test -p codex-app-server`
- `cargo check -p codex-app-server`
- `just fix -p codex-app-server`
Owen Lin