**Stack position:** [5 of 7]
## Summary
This PR adds `Op::ThreadSettings`, a queued settings-only update
mechanism for changing stored thread settings without starting a new
turn. It also removes the legacy `Op::OverrideTurnContext` in the same
layer, so reviewers can see the replacement and deletion together.
## Changes
- Add `Op::ThreadSettings` for settings-only queued updates.
- Emit `ThreadSettingsApplied` with the effective thread settings
snapshot after core applies an update.
- Route settings-only updates through the same submission queue as user
input.
- Migrate remaining `OverrideTurnContext` tests and callers to the
queued `Op::ThreadSettings` path.
- Delete `Op::OverrideTurnContext` from the core protocol and submission
loop.
This stack addresses #20656 and #22090.
## Stack
1. [1 of 7] [Add thread settings to
UserInput](https://github.com/openai/codex/pull/23080)
2. [2 of 7] [Remove
UserInputWithTurnContext](https://github.com/openai/codex/pull/23081)
3. [3 of 7] [Remove
UserTurn](https://github.com/openai/codex/pull/23075)
4. [4 of 7] [Placeholder for OverrideTurnContext
cleanup](https://github.com/openai/codex/pull/23087)
5. [5 of 7] [Replace OverrideTurnContext with
ThreadSettings](https://github.com/openai/codex/pull/22508) (this PR)
6. [6 of 7] [Add app-server thread settings
API](https://github.com/openai/codex/pull/22509)
7. [7 of 7] [Sync TUI thread
settings](https://github.com/openai/codex/pull/22510)
## Why
Windows can reject plugin cache upgrades when a running MCP server still
has its working directory inside the currently active plugin version.
The existing cache refresh path replaces
`plugins/cache/<marketplace>/<plugin>` as a whole, so a live handle
under the old version can make an otherwise ordinary version bump fail.
This PR keeps the existing plugin-selection model intact while making
version bumps less disruptive.
## What changed
- When installing a new version beside an existing plugin cache root,
move only the staged version directory into place instead of replacing
the whole plugin root.
- Best-effort prune older sibling version directories after the new
version is activated.
- Preserve the existing whole-root replacement path for first installs
and same-version refreshes.
- Add regression coverage for upgrading from `1.0.0` to `2.0.0` without
replacing the plugin root.
## Verification
- `cargo test -p codex-core-plugins install_with_new_version`
- `cargo fmt --package codex-core-plugins --check`
## Why
`run_turn` had accumulated the turn-scoped skill, plugin, app, MCP,
connector-selection, and analytics setup inline. That made the
orchestration path harder to scan even though the actual turn item
injection still needs to stay in `run_turn` so ordering is explicit.
## What changed
This extracts that setup into `build_skills_and_plugins`, which returns
the combined injection `ResponseItem`s and the explicitly enabled
connector IDs. `run_turn` now keeps the required orchestration pieces:
context update recording, user input handling, connector selection
merge, and the explicit per-item `record_conversation_items` calls for
injection items.
The refactor keeps the change LOC-neutral in `core/src/session/turn.rs`
and preserves the existing response-item based injection path.
## Validation
- `cargo test -p codex-core collect_explicit_app_ids_from_skill_items`
- `just fix -p codex-core`
**Stack position:** [1 of 7]
## Summary
The first three PRs in this stack are a cleanup pass before the actual
thread settings API work.
Today, core has several overlapping "user input" ops: `UserInput`,
`UserInputWithTurnContext`, and `UserTurn`. They differ mostly in how
much next-turn state they carry, which makes the later queued thread
settings update harder to reason about and review.
This PR starts that cleanup by adding the shared
`ThreadSettingsOverrides` payload and allowing `Op::UserInput` to carry
it. Existing variants remain in place here, so this layer is mostly a
behavior-preserving API shape change plus mechanical constructor
updates.
## End State After PR3
By the end of PR3, `Op::UserInput` is the only "user input" core op. It
can carry optional thread settings overrides for callers that need to
update stored defaults with a turn, while callers without updates use
empty settings. `Op::UserInputWithTurnContext` and `Op::UserTurn` are
deleted.
## End State After PR5
By the end of PR5, core will have only two ops for this area:
- `Op::UserInput` for user-input-bearing submissions.
- `Op::ThreadSettings` for settings-only updates.
## Stack
1. [1 of 7] [Add thread settings to
UserInput](https://github.com/openai/codex/pull/23080) (this PR)
2. [2 of 7] [Remove
UserInputWithTurnContext](https://github.com/openai/codex/pull/23081)
3. [3 of 7] [Remove
UserTurn](https://github.com/openai/codex/pull/23075)
4. [4 of 7] [Placeholder for OverrideTurnContext
cleanup](https://github.com/openai/codex/pull/23087)
5. [5 of 7] [Replace OverrideTurnContext with
ThreadSettings](https://github.com/openai/codex/pull/22508)
6. [6 of 7] [Add app-server thread settings
API](https://github.com/openai/codex/pull/22509)
7. [7 of 7] [Sync TUI thread
settings](https://github.com/openai/codex/pull/22510)
## Summary
- mark `ToolSearch` as removed and ignore stale config writes for its
legacy key
- make search tool exposure depend only on model capability, not a
feature toggle
- remove app-server enablement support and prune now-obsolete test
coverage/setup
## Verification
- `cargo test -p codex-features`
- `cargo test -p codex-tools`
- `cargo test -p codex-core search_tool_requires_model_capability`
- `cargo test -p codex-app-server experimental_feature_enablement_set_`
## Notes
- This keeps the legacy config key as a no-op for compatibility while
removing the ability to toggle the behavior off cleanly.
- No developer-facing docs update outside the touched app-server README
was needed.
Deletes the skill env var dependency prompt feature and its runtime
path. env_var entries in skill dependency metadata are now silently
ignored during skill loading.
## Why
Compaction now installs replacement history inside the session, but the
turn and compaction callers were still reaching into
`ModelClientSession` to reset websocket transport state after that
install. That made a transport-level reset part of the compaction API
even though websocket incremental request selection already checks
whether the next request is a strict extension of the previous one and
falls back to a full `response.create` when it is not.
## What changed
- Removed the compaction-side calls to `reset_websocket_session` from
`compact.rs` and `session/turn.rs`.
- Simplified pre-sampling and mid-turn compaction helpers so they return
`CodexResult<()>` instead of carrying a reset flag.
- Made `ModelClientSession::reset_websocket_session` private to
`client.rs`, leaving only the websocket timeout recovery path inside the
client as a caller.
## Validation
- `cargo test -p codex-core --test all
responses_websocket_creates_on_non_prefix`
- `cargo test -p codex-core --test all
steered_user_input_waits_for_model_continuation_after_mid_turn_compact`
- `cargo test -p codex-core --test all
pre_sampling_compact_runs_on_switch_to_smaller_context_model`
## 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
- Follows #20949.
- The above moved `thread_source` attribution from the reducer to
explicit caller provided metadata
- The `codex exec` path still omitted this metadata, leaving
exec-created threads without `thread_source`
## What Changed
- Ensures exec threads are marked as user created (`thread_source =
"user"`)
- Preserves thread-source metadata in exec’s startup session event
## Verification
- Updated unit tests to validate exec `thread_source` propagation.
- `cargo +1.93.0 test -p codex-exec --manifest-path codex-rs/Cargo.toml`
- `cargo +1.93.1 build -p codex-cli --manifest-path codex-rs/Cargo.toml`
- Validated locally with a freshly built `codex exec` run:
- Startup logs showed `thread_source: Some(User)`.
- Rollout metadata recorded `"thread_source":"user"`.
Eric Traut