fix(setup): enable writes the enabled flag to the resolved settings scope

On a repo disabled at the project level, entire enable --checkpoint-remote ... (no --project) reported success but left .entire/settings.json enabled=false: the strategy write resolved to the existing project settings.json while the enabled flag was written to settings.local.json (raw opts.UseProjectSettings bool). Resolve the enable target with settingsTargetFile, matching where the strategy options were written, so the enabled flag lands in the same file.

Closes #1140