Repo config.toml cannot override plugins / skills enabled state from user config.toml

What version of Codex CLI is running?

codex-cli 0.144.4

What subscription do you have?

Free

Which model were you using?

_No response_

What platform is your computer?

_No response_

What terminal emulator and version are you using (if applicable)?

_No response_

Codex doctor report

What issue are you seeing?

When trying to override plugin or skill configuration from a repository config.toml, I found that the enabled flag under plugins and skills does not take effect.

The same issue also appears when trying to override the configuration via the -c command-line option.

What steps can reproduce the bug?

1. Configure the user config

~/.codex/config.toml

[plugins."expo@openai-api-curated"]
enabled = true

2. Configure the repository config

<repo>/.codex/config.toml

[plugins."expo@openai-api-curated"]
enabled = false

3. Start Codex in the repository

The expo plugin is still enabled.

What is the expected behavior?

The repository config.toml should override the user config.toml, so the expo plugin should be disabled.

Likewise, overriding the configuration with -c should also work.

Additional information

_No response_