## 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
`codex-rs/app-server-protocol/src/protocol/v2.rs` had grown into a
single ~12k-line definition file for the entire app-server v2 API.
This is purely a mechanical refactor to break up the monolithic `v2.rs`
file that contains all app-server API v2 types into more modular files,
grouped by resource (e.g. account, thread, turn, etc.).
`just write-app-server-schema` shows no real changes, so we can be sure
that this is purely an internal organizational change.
## What changed
- Replaced the monolithic `protocol/v2.rs` with a `protocol/v2/` module
tree and a small `mod.rs` that only declares and reexports modules.
- Grouped v2 API definitions by conceptual owner, including `account`,
`apps`, `collaboration_mode`, `command_exec`, `config`, `device_key`,
`experimental_feature`, `feedback`, `fs`, `hook`, `item`, `mcp`,
`model`, `notification`, `permissions`, `plugin`, `process`, `realtime`,
`review`, `thread`, `thread_data`, `turn`, and `windows_sandbox`.
- Moved v2 tests into `protocol/v2/tests.rs` so `mod.rs` stays small.
- Kept shared protocol helpers in `protocol/v2/shared.rs`, including the
enum mirroring macro and common cross-resource types.
- Co-located resource-specific notifications and server-request payloads
with the modules that own those resources.
- Regenerated app-server protocol schema fixtures. The schema diffs are
non-semantic newline-only changes after the refactor.
## Verification
- `cargo check -p codex-app-server-protocol`
- `cargo test -p codex-app-server-protocol`
- `just write-app-server-schema`
Michael Bolin