app-server: refresh live threads from latest config snapshot

[jif-oai]

Why

App-server config writes were leaving existing threads partially stale. After a config mutation, the app-server told each live thread to run Op::ReloadUserConfig, but that path only re-read the user config.toml layer. Settings that came from the app-server's materialized config snapshot did not propagate to existing threads until restart.

This change prevent a FS access from core for CCA.

What changed

• add CodexThread::refresh_runtime_config() and Session::refresh_runtime_config() so the app-server can push a freshly rebuilt config snapshot into a live thread
• rebuild the latest config with each thread's cwd after config mutations, then refresh the thread from that snapshot instead of asking it to reload only config.toml
• keep session-static settings unchanged during refresh, while updating runtime-refreshable state such as the config layer stack, tool_suggest, and derived hook/plugin/skill state
• keep reload_user_config_layer() as the file-backed fallback for legacy local reload flows, but route the shared refresh logic through the new runtime refresh path

Testing

• add a session test that verifies refresh_runtime_config() rebuilds hooks from refreshed config
• add a session test that verifies runtime-refreshable fields update while session-static settings like model and notify stay unchanged

[jif-oai]

@codex review

[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. 👍

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[jif-oai]

@codex review

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: ad56d24eda

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[jif-oai]

@codex review

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 85fe8faa83

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".