with_integration_setting recomputed invoke_separator from the raw
parsed_options argument. When only script_type changes (parsed_options and
raw_options both None), the previously-stored parsed_options are retained on
the setting, but the separator was derived from the None argument — dropping
an options-dependent separator (e.g. Copilot --skills -> "-") back to the
default ".", desynchronizing invoke_separator from the stored options.
Derive the separator from current.get("parsed_options") — the options
actually stored after the update — so it stays consistent in every branch.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>