settings: keep configure --local from re-enabling a disabled repo

A settings file without an "enabled" key loads as enabled (the default), and every local field update saved that default back as an explicit "enabled": true. In a repository the project file disables, running entire configure --local --telemetry=false (or any other local setting change) therefore created a local override that turned Entire back on.

SaveLocal now writes "enabled" only when the settings state it: the file they were loaded from had the key, or SetEnabled was called. The enable paths use SetEnabled, so entire enable --local still writes it.