applyToolConfig() unconditionally set question permission based only on
OPENCODE_CLI_RUN_MODE, ignoring the question:deny already configured via
OPENCODE_CONFIG_CONTENT. This caused agents to hang in headless environments
(e.g. Maestro Auto Run) where the host sets question:deny but does not
know about the plugin-internal OPENCODE_CLI_RUN_MODE variable.
Read permission.question from OPENCODE_CONFIG_CONTENT and give it highest
priority: config deny > CLI run mode deny > default allow.
