## What is flaky
The Windows shell-driven integration tests in `codex-rs/core` were
intermittently unstable, especially:
- `apply_patch_cli_can_use_shell_command_output_as_patch_input`
- `websocket_test_codex_shell_chain`
- `websocket_v2_test_codex_shell_chain`
## Why it was flaky
These tests were exercising real shell-tool flows through whichever
shell Codex selected on Windows, and the `apply_patch` test also nested
a PowerShell read inside `cmd /c`.
There were multiple independent sources of nondeterminism in that setup:
- The test harness depended on the model-selected Windows shell instead
of pinning the shell it actually meant to exercise.
- `cmd.exe /c powershell.exe -Command "..."` is quoting-sensitive; on CI
that could leave the read command wrapped as a literal string instead of
executing it.
- Even after getting the quoting right, PowerShell could emit CLIXML
progress records like module-initialization output onto stdout.
- The `apply_patch` test was building a patch directly from shell
stdout, so any quoting artifact or progress noise corrupted the patch
input.
So the failures were driven by shell startup and output-shape variance,
not by the `apply_patch` or websocket logic themselves.
## How this PR fixes it
- Add a test-only `user_shell_override` path so Windows integration
tests can pin `cmd.exe` explicitly.
- Use that override in the websocket shell-chain tests and in the
`apply_patch` harness.
- Change the nested Windows file read in
`apply_patch_cli_can_use_shell_command_output_as_patch_input` to a UTF-8
PowerShell `-EncodedCommand` script.
- Run that nested PowerShell process with `-NonInteractive`, set
`$ProgressPreference = 'SilentlyContinue'`, and read the file with
`[System.IO.File]::ReadAllText(...)`.
## Why this fix fixes the flakiness
The outer harness now runs under a deterministic shell, and the inner
PowerShell read no longer depends on fragile `cmd` quoting or on
progress output staying quiet by accident. The shell tool returns only
the file contents, so patch construction and websocket assertions depend
on stable test inputs instead of on runner-specific shell behavior.
---------
Co-authored-by: Ahmed Ibrahim <219906144+aibrahim-oai@users.noreply.github.com>
Co-authored-by: Codex <noreply@openai.com>
## Why
Once the repo-local lint exists, `codex-rs` needs to follow the
checked-in convention and CI needs to keep it from drifting. This commit
applies the fallback `/*param*/` style consistently across existing
positional literal call sites without changing those APIs.
The longer-term preference is still to avoid APIs that require comments
by choosing clearer parameter types and call shapes. This PR is
intentionally the mechanical follow-through for the places where the
existing signatures stay in place.
After rebasing onto newer `main`, the rollout also had to cover newly
introduced `tui_app_server` call sites. That made it clear the first cut
of the CI job was too expensive for the common path: it was spending
almost as much time installing `cargo-dylint` and re-testing the lint
crate as a representative test job spends running product tests. The CI
update keeps the full workspace enforcement but trims that extra
overhead from ordinary `codex-rs` PRs.
## What changed
- keep a dedicated `argument_comment_lint` job in `rust-ci`
- mechanically annotate remaining opaque positional literals across
`codex-rs` with exact `/*param*/` comments, including the rebased
`tui_app_server` call sites that now fall under the lint
- keep the checked-in style aligned with the lint policy by using
`/*param*/` and leaving string and char literals uncommented
- cache `cargo-dylint`, `dylint-link`, and the relevant Cargo
registry/git metadata in the lint job
- split changed-path detection so the lint crate's own `cargo test` step
runs only when `tools/argument-comment-lint/*` or `rust-ci.yml` changes
- continue to run the repo wrapper over the `codex-rs` workspace, so
product-code enforcement is unchanged
Most of the code changes in this commit are intentionally mechanical
comment rewrites or insertions driven by the lint itself.
## Verification
- `./tools/argument-comment-lint/run.sh --workspace`
- `cargo test -p codex-tui-app-server -p codex-tui`
- parsed `.github/workflows/rust-ci.yml` locally with PyYAML
---
* -> #14652
* #14651
We regularly get bug reports from users who mistakenly have the
`OPENAI_BASE_URL` environment variable set. This PR deprecates this
environment variable in favor of a top-level config key
`openai_base_url` that is used for the same purpose. By making it a
config key, it will be more visible to users. It will also participate
in all of the infrastructure we've added for layered and managed
configs.
Summary
- introduce the `openai_base_url` top-level config key, update
schema/tests, and route the built-in openai provider through it while
- fall back to deprecated `OPENAI_BASE_URL` env var but warn user of
deprecation when no `openai_base_url` config key is present
- update CLI, SDK, and TUI code to prefer the new config path (with a
deprecated env-var fallback) and document the SDK behavior change
## Why
PR #13783 moved the `codex.rs` unit tests into `codex_tests.rs`. This
applies the same extraction pattern across the rest of `codex-rs/core`
so the production modules stay focused on runtime code instead of large
inline test blocks.
Keeping the tests in sibling files also makes follow-up edits easier to
review because product changes no longer have to share a file with
hundreds or thousands of lines of test scaffolding.
## What changed
- replaced each inline `mod tests { ... }` in `codex-rs/core/src/**`
with a path-based module declaration
- moved each extracted unit test module into a sibling `*_tests.rs`
file, using `mod_tests.rs` for `mod.rs` modules
- preserved the existing `cfg(...)` guards and module-local structure so
the refactor remains structural rather than behavioral
## Testing
- `cargo test -p codex-core --lib` (`1653 passed; 0 failed; 5 ignored`)
- `just fix -p codex-core`
- `cargo fmt --check`
- `cargo shear`
## Summary
This PR keeps app-server RPC request trace context alive for the full
lifetime of the work that request kicks off (e.g. for `thread/start`,
this is `app-server rpc handler -> tokio background task -> core op
submissions`). Previously we lose trace lineage once the request handler
returns or hands work off to background tasks.
This approach is especially relevant for `thread/start` and other RPC
handlers that run in a non-blocking way. In the near future we'll most
likely want to make all app-server handlers run in a non-blocking way by
default, and only queue operations that must operate in order (e.g.
thread RPCs per thread?), so we want to make sure tracing in app-server
just generally works.
Depends on https://github.com/openai/codex/pull/14300
**Before**
<img width="155" height="207" alt="image"
src="https://github.com/user-attachments/assets/c9487459-36f1-436c-beb7-fafeb40737af"
/>
**After**
<img width="299" height="337" alt="image"
src="https://github.com/user-attachments/assets/727392b2-d072-4427-9dc4-0502d8652dea"
/>
## What changed
- Keep request-scoped trace context around until we send the final
response or error, or the connection closes.
- Thread that trace context through detached `thread/start` work so
background startup stays attached to the originating request.
- Pass request trace context through to downstream core operations,
including:
- thread creation
- resume/fork flows
- turn submission
- review
- interrupt
- realtime conversation operations
- Add tracing tests that verify:
- remote W3C trace context is preserved for `thread/start`
- remote W3C trace context is preserved for `turn/start`
- downstream core spans stay under the originating request span
- request-scoped tracing state is cleaned up correctly
- Clean up shutdown behavior so detached background tasks and spawned
threads are drained before process exit.
## Why
to support a new bring your own search tool in Responses
API(https://developers.openai.com/api/docs/guides/tools-tool-search#client-executed-tool-search)
we migrating our bm25 search tool to use official way to execute search
on client and communicate additional tools to the model.
## What
- replace the legacy `search_tool_bm25` flow with client-executed
`tool_search`
- add protocol, SSE, history, and normalization support for
`tool_search_call` and `tool_search_output`
- return namespaced Codex Apps search results and wire namespaced
follow-up tool calls back into MCP dispatch
Follow-up to [#13388](https://github.com/openai/codex/pull/13388). This
uses the same general fix pattern as
[#12421](https://github.com/openai/codex/pull/12421), but in the
`codex-core` compact/resume/fork path.
## Why
`compact_resume_after_second_compaction_preserves_history` started
overflowing the stack on Windows CI after `#13388`.
The important part is that this was not a compaction-recursion bug. The
test exercises a path with several thin `async fn` wrappers around much
larger thread-spawn, resume, and fork futures. When one `async fn`
awaits another inline, the outer future stores the callee future as part
of its own state machine. In a long wrapper chain, that means a caller
can accidentally inline a lot more state than the source code suggests.
That is exactly what was happening here:
- `ThreadManager` convenience methods such as `start_thread`,
`resume_thread_from_rollout`, and `fork_thread` were inlining the larger
spawn/resume futures beneath them.
- `core_test_support::test_codex` added another wrapper layer on top of
those same paths.
- `compact_resume_fork` adds a few more helpers, and this particular
test drives the resume/fork path multiple times.
On Windows, that was enough to push both the libtest thread and Tokio
worker threads over the edge. The previous 8 MiB test-thread workaround
proved the failure was stack-related, but it did not address the
underlying future size.
## How This Was Debugged
The useful debugging pattern here was to turn the CI-only failure into a
local low-stack repro.
1. First, remove the explicit large-stack harness so the test runs on
the normal `#[tokio::test]` path.
2. Build the test binary normally.
3. Re-run the already-built `tests/all` binary directly with
progressively smaller `RUST_MIN_STACK` values.
Running the built binary directly matters: it keeps the reduced stack
size focused on the test process instead of also applying it to `cargo`
and `rustc`.
That made it possible to answer two questions quickly:
- Does the failure still reproduce without the workaround? Yes.
- Does boxing the wrapper futures actually buy back stack headroom? Also
yes.
After this change, the built test binary passes with
`RUST_MIN_STACK=917504` and still overflows at `786432`, which is enough
evidence to justify removing the explicit 8 MiB override while keeping a
deterministic low-stack repro for future debugging.
If we hit a similar issue again, the first places to inspect are thin
`async fn` wrappers that mostly forward into a much larger async
implementation.
## `Box::pin()` Primer
`async fn` compiles into a state machine. If a wrapper does this:
```rust
async fn wrapper() {
inner().await;
}
```
then `wrapper()` stores the full `inner()` future inline as part of its
own state.
If the wrapper instead does this:
```rust
async fn wrapper() {
Box::pin(inner()).await;
}
```
then the child future lives on the heap, and the outer future only
stores a pinned pointer to it. That usually trades one allocation for a
substantially smaller outer future, which is exactly the tradeoff we
want when the problem is stack pressure rather than raw CPU time.
Useful references:
-
[`Box::pin`](https://doc.rust-lang.org/std/boxed/struct.Box.html#method.pin)
- [Async book:
Pinning](https://rust-lang.github.io/async-book/04_pinning/01_chapter.html)
## What Changed
- Boxed the wrapper futures in `core/src/thread_manager.rs` around
`start_thread`, `resume_thread_from_rollout`, `fork_thread`, and the
corresponding `ThreadManagerState` spawn helpers so callers no longer
inline the full spawn/resume state machine through multiple layers.
- Boxed the matching test-only wrapper futures in
`core/tests/common/test_codex.rs` and
`core/tests/suite/compact_resume_fork.rs`, which sit directly on top of
the same path.
- Restored `compact_resume_after_second_compaction_preserves_history` in
`core/tests/suite/compact_resume_fork.rs` to a normal `#[tokio::test]`
and removed the explicit `TEST_STACK_SIZE_BYTES` thread/runtime sizing.
- Simplified a tiny helper in `compact_resume_fork` by making
`fetch_conversation_path()` synchronous, which removes one more
unnecessary future layer from the test path.
## Verification
- `cargo test -p codex-core --test all
suite::compact_resume_fork::compact_resume_after_second_compaction_preserves_history
-- --exact --nocapture`
- `cargo test -p codex-core --test all suite::compact_resume_fork --
--nocapture`
- Re-ran the built `codex-core` `tests/all` binary directly with reduced
stack sizes:
- `RUST_MIN_STACK=917504` passes
- `RUST_MIN_STACK=786432` still overflows
- `cargo test -p codex-core`
- Still fails locally in unrelated existing integration areas that
expect the `codex` / `test_stdio_server` binaries or hit the existing
`search_tool` wiremock mismatches.
## Summary
- reuse the parent shell snapshot when spawning/forking/resuming
`SessionSource::SubAgent(SubAgentSource::ThreadSpawn { .. })` sessions
- plumb inherited snapshot through `AgentControl -> ThreadManager ->
Codex::spawn -> SessionConfiguration`
- skip shell snapshot refresh on cwd updates for thread-spawn subagents
so inherited snapshots are not replaced
## Why
- avoids per-subagent shell snapshot creation and cleanup work
- keeps thread-spawn subagents on the parent snapshot path, matching the
intended parent/child snapshot model
## Validation
- `just fmt` (in `codex-rs`)
- `cargo test -p codex-core --no-run`
- `cargo test -p codex-core spawn_agent -- --nocapture`
- `cargo test -p codex-core --test all
suite::agent_jobs::spawn_agents_on_csv_runs_and_exports`
## Notes
- full `cargo test -p codex-core --test all` was left running separately
for broader verification
Co-authored-by: Codex <noreply@openai.com>
## Summary
- record a realtime close developer message when a new realtime session
replaces an active one
- assert the replacement marker through the mocked responses request
path
---------
Co-authored-by: Codex <noreply@openai.com>
Co-authored-by: Charles Cunningham <ccunningham@openai.com>
Support loading plugins.
Plugins can now be enabled via [plugins.<name>] in config.toml. They are
loaded as first-class entities through PluginsManager, and their default
skills/ and .mcp.json contributions are integrated into the existing
skills and MCP flows.
## Summary
- bundle contextual prompt injection into at most one developer message
plus one contextual user message in both:
- per-turn settings updates
- initial context insertion
- preserve `<model_switch>` across compaction by rebuilding it through
canonical initial-context injection, instead of relying on
strip/reattach hacks
- centralize contextual user fragment detection in one shared definition
table and reuse it for parsing/compaction logic
- keep `AGENTS.md` in its natural serialized format:
- `# AGENTS.md instructions for {dirname}`
- `<INSTRUCTIONS>...</INSTRUCTIONS>`
- simplify related tests/helpers and accept the expected snapshot/layout
updates from bundled multi-part messages
## Why
The goal is to converge toward a simpler, more intentional prompt shape
where contextual updates are consistently represented as one developer
envelope plus one contextual user envelope, while keeping parsing and
compaction behavior aligned with that representation.
## Notable details
- the temporary `SettingsUpdateEnvelope` wrapper was removed; these
paths now return `Vec<ResponseItem>` directly
- local/remote compaction no longer rely on model-switch strip/restore
helpers
- contextual user detection is now driven by shared fragment definitions
instead of ad hoc matcher assembly
- AGENTS/user instructions are still the same logical context; only the
synthetic `<user_instructions>` wrapper was replaced by the natural
AGENTS text format
## Testing
- `just fmt`
- `cargo test -p codex-app-server
codex_message_processor::tests::extract_conversation_summary_prefers_plain_user_messages
-- --exact`
- `cargo test -p codex-core
compact::tests::collect_user_messages_filters_session_prefix_entries
--lib -- --exact`
- `cargo test -p codex-core --test all
'suite::compact::snapshot_request_shape_pre_turn_compaction_strips_incoming_model_switch'
-- --exact`
- `cargo test -p codex-core --test all
'suite::compact_remote::snapshot_request_shape_remote_pre_turn_compaction_strips_incoming_model_switch'
-- --exact`
- `cargo test -p codex-core --test all
'suite::client::includes_apps_guidance_as_developer_message_when_enabled'
-- --exact`
- `cargo test -p codex-core --test all
'suite::client::includes_developer_instructions_message_in_request' --
--exact`
- `cargo test -p codex-core --test all
'suite::client::includes_user_instructions_message_in_request' --
--exact`
- `cargo test -p codex-core --test all
'suite::client::resume_includes_initial_messages_and_sends_prior_items'
-- --exact`
- `cargo test -p codex-core --test all
'suite::review::review_input_isolated_from_parent_history' -- --exact`
- `cargo test -p codex-exec --test all
'suite::resume::exec_resume_last_respects_cwd_filter_and_all_flag' --
--exact`
- `cargo test -p core_test_support
context_snapshot::tests::full_text_mode_preserves_unredacted_text --
--exact`
## Notes
- I also ran several targeted `compact`, `compact_remote`,
`prompt_caching`, `model_visible_layout`, and `event_mapping` tests
while iterating on prompt-shape changes.
- I have not claimed a clean full-workspace `cargo test` from this
environment because local sandbox/resource conditions have previously
produced unrelated failures in large workspace runs.
## Summary
- allow `request_user_input` in Default collaboration mode as well as
Plan
- update the Default-mode instructions to prefer assumptions first and
use `request_user_input` only when a question is unavoidable
- update request_user_input and app-server tests to match the new
Default-mode behavior
- refactor collaboration-mode availability plumbing into
`CollaborationModesConfig` for future mode-related flags
## Codex author
`codex resume 019c9124-ed28-7c13-96c6-b916b1c97d49`
Add service name to the app-server so that the app can use it's own
service name
This is on thread level because later we might plan the app-server to
become a singleton on the computer
TL;DR
Add top-level `model_catalog_json` config support so users can supply a
local model catalog override from a JSON file path (including adding new
models) without backend changes.
### Problem
Codex previously had no clean client-side way to replace/overlay model
catalog data for local testing of model metadata and new model entries.
### Fix
- Add top-level `model_catalog_json` config field (JSON file path).
- Apply catalog entries when resolving `ModelInfo`:
1. Base resolved model metadata (remote/fallback)
2. Catalog overlay from `model_catalog_json`
3. Existing global top-level overrides (`model_context_window`,
`model_supports_reasoning_summaries`, etc.)
### Note
Will revisit per-field overrides in a follow-up
### Tests
Added tests
The issue was that the file_watcher never unsubscribe a file watch. All
of them leave in the owning of the ThreadManager. As a result, for each
newly created thread we create a new file watcher but this one never get
deleted even if we close the thread. On Unix system, a file watcher uses
an `inotify` and after some time we end up having consumed all of them.
This PR adds a mechanism to unsubscribe a file watcher when a thread is
dropped
rm `remote_models` feature flag.
We see issues like #11527 when a user has `remote_models` disabled, as
we always use the default fallback `ModelInfo`. This causes issues with
model performance.
Builds on #11690, which helps by warning the user when they are using
the default fallback. This PR will make that happen much less frequently
as an accidental consequence of disabling `remote_models`.
This PR adds an experimental `persist_extended_history` bool flag to
app-server thread APIs so rollout logs can retain a richer set of
EventMsgs for non-lossy Thread > Turn > ThreadItems reconstruction (i.e.
on `thread/resume`).
### Motivation
Today, our rollout recorder only persists a small subset (e.g. user
message, reasoning, assistant message) of `EventMsg` types, dropping a
good number (like command exec, file change, etc.) that are important
for reconstructing full item history for `thread/resume`, `thread/read`,
and `thread/fork`.
Some clients want to be able to resume a thread without lossiness. This
lossiness is primarily a UI thing, since what the model sees are
`ResponseItem` and not `EventMsg`.
### Approach
This change introduces an opt-in `persist_full_history` flag to preserve
those events when you start/resume/fork a thread (defaults to `false`).
This is done by adding an `EventPersistenceMode` to the rollout
recorder:
- `Limited` (existing behavior, default)
- `Extended` (new opt-in behavior)
In `Extended` mode, persist additional `EventMsg` variants needed for
non-lossy app-server `ThreadItem` reconstruction. We now store the
following ThreadItems that we didn't before:
- web search
- command execution
- patch/file changes
- MCP tool calls
- image view calls
- collab tool outcomes
- context compaction
- review mode enter/exit
For **command executions** in particular, we truncate the output using
the existing `truncate_text` from core to store an upper bound of 10,000
bytes, which is also the default value for truncating tool outputs shown
to the model. This keeps the size of the rollout file and command
execution items returned over the wire reasonable.
And we also persist `EventMsg::Error` which we can now map back to the
Turn's status and populates the Turn's error metadata.
#### Updates to EventMsgs
To truly make `thread/resume` non-lossy, we also needed to persist the
`status` on `EventMsg::CommandExecutionEndEvent` and
`EventMsg::PatchApplyEndEvent`. Previously it was not obvious whether a
command failed or was declined (similar for apply_patch). These
EventMsgs were never persisted before so I made it a required field.
## Why
`codex-core` was being built in multiple feature-resolved permutations
because test-only behavior was modeled as crate features. For a large
crate, those permutations increase compile cost and reduce cache reuse.
## Net Change
- Removed the `test-support` crate feature and related feature wiring so
`codex-core` no longer needs separate feature shapes for test consumers.
- Standardized cross-crate test-only access behind
`codex_core::test_support`.
- External test code now imports helpers from
`codex_core::test_support`.
- Underlying implementation hooks are kept internal (`pub(crate)`)
instead of broadly public.
## Outcome
- Fewer `codex-core` build permutations.
- Better incremental cache reuse across test targets.
- No intended production behavior change.
Summary
- add the new resume_agent collab tool path through core, protocol, and
the app server API, including the resume events
- update the schema/TypeScript definitions plus docs so resume_agent
appears in generated artifacts and README
- note that resumed agents rehydrate rollout history without overwriting
their base instructions
Testing
- Not run (not requested)
Add a centralized FileWatcher in codex-core (using notify) that watches
skill roots from the config layer stack (recursive)
Send `SkillsChanged` events when relevant file system changes are
detected
On `SkillsChanged`:
* Invalidate the skills cache immediately in ThreadManager
* Emit EventMsg::SkillsUpdateAvailable to active sessions
~~* Broadcast a new app-server notification:
SkillsListUpdatedNotification~~
This change does not inject new items into the event stream. That means
the agent will not know about new skills, so it won't be able to
implicitly invoke new skills. It also won't know about changes to
existing skills, so if it has already read the contents of a modified
skill, it will not honor the new behavior.
This change also does not detect modifications to AGENTS.md.
I plan to address these limitations in a follow-on PR modeled after
#9985. Injection of new skills and AGENTS was deemed to risky, hence the
need to split the feature into two stages. The changes in this PR were
designed to easily accommodate the second stage once we have some other
foundational changes in place.
Testing: In addition to automated tests, I did manual testing to confirm
that newly-created skills, deleted skills, and renamed skills are
reflected in the TUI skill picker menu. Also confirmed that
modifications to behaviors for explicitly-invoked skills are honored.
---------
Co-authored-by: Xin Lin <xl@openai.com>
### What
add wiring for `phase` field on `ResponseItem::Message` to lay
groundwork for differentiating model preambles and final messages.
currently optional.
follows pattern in #9698.
updated schemas with `just write-app-server-schema` so we can see type
changes.
### Tests
Updated existing tests for SSE parsing and hydrating from history
## Summary
Add dynamic tool injection to thread startup in API v2, wire dynamic
tool calls through the app server to clients, and plumb responses back
into the model tool pipeline.
### Flow (high level)
- Thread start injects `dynamic_tools` into the model tool list for that
thread (validation is done here).
- When the model emits a tool call for one of those names, core raises a
`DynamicToolCallRequest` event.
- The app server forwards it to the client as `item/tool/call`, waits
for the client’s response, then submits a `DynamicToolResponse` back to
core.
- Core turns that into a `function_call_output` in the next model
request so the model can continue.
### What changed
- Added dynamic tool specs to v2 thread start params and protocol types;
introduced `item/tool/call` (request/response) for dynamic tool
execution.
- Core now registers dynamic tool specs at request time and routes those
calls via a new dynamic tool handler.
- App server validates tool names/schemas, forwards dynamic tool call
requests to clients, and publishes tool outputs back into the session.
- Integration tests
Keep an unmasked base collaboration mode and apply the active mask on
demand. Simplify the TUI mask helpers and update tests/docs to match the
mask contract.
# External (non-OpenAI) Pull Request Requirements
Before opening this Pull Request, please read the dedicated
"Contributing" markdown file or your PR may be closed:
https://github.com/openai/codex/blob/main/docs/contributing.md
If your PR conforms to our contribution guidelines, replace this text
with a detailed and high quality description of your changes.
Include a link to a bug report or enhancement request.
This PR is in the scope of multi-agent work.
An agent (=thread) can now spawn other agents. Those other agents are
not attached to any clients. We need a way to make sure that the clients
are aware of the new threads to look at (for approval for example). This
PR adds a channel to the `ThreadManager` that pushes the ID of those
newly created agents such that the client (here the app-server) can also
subscribe to those ones.
Have only the following Methods:
- `list_models`: getting current available models
- `try_list_models`: sync version no refresh for tui use
- `get_default_model`: get the default model (should be tightened to
core and received on session configuration)
- `get_model_info`: get `ModelInfo` for a specific model (should be
tightened to core but used in tests)
- `refresh_if_new_etag`: trigger refresh on different etags
Also move the cache to its own struct
- Add a single builder for developer permissions messaging that accepts
SandboxPolicy and approval policy. This builder now drives the developer
“permissions” message that’s injected at session start and any time
sandbox/approval settings change.
- Trim EnvironmentContext to only include cwd, writable roots, and
shell; removed sandbox/approval/network duplication and adjusted XML
serialization and tests accordingly.
Follow-up: adding a config value to replace the developer permissions
message for custom sandboxes.
### Summary
* Added `mcpServer/refresh` command to inform app servers and active
threads to refresh mcpServer on next turn event.
* Added `pending_mcp_server_refresh_config` to codex core so that if the
value is populated, we reinitialize the mcp server manager on the thread
level.
* The config is updated on `mcpServer/refresh` command which we iterate
through threads and provide with the latest config value after last
write.
