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A running script reached `prefs.set` through `app.run` and could turn on Settings > Scripting & Expressions > Allow Scripts to Write Files and Access Network (or turn off Warn User When Executing Files), which the File, Socket and system.callSystem gates then read: the permission the user withheld was the script's to take. Commands a script issues now go through `Session::execute_for_script`, which marks the session as running for a script for the command and everything it runs (engine.batch, ScriptUI callbacks, scheduled tasks). While it is, `prefs.set` refuses any change that would leave the Application Scripting settings different (compared on the resulting settings, so dotted keys, whole-page objects and batches are all covered), and a script's `prefs.reset` keeps them as the user set them. Command scripts read from a file (File > Scripts > Run Script File... with .json/.jsonl) count as scripts too. The UI, CLI, control channel and MCP still change them. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01QiAJeFttZp83Fh7YuzAR5f