fix(setup): stop enable/disable from leaking local overrides into project settings

runEnable/runDisable loaded the merged LoadEntireSettings view (project + settings.local.json overrides flattened together), flipped the enabled bit, and wrote the whole struct back. Once #1140 made a bare entire enable resolve to settings.json when the project file already exists, this started writing local-only overrides (local_dev, log_level, personal strategy_options/checkpoint_remote, ...) into the shared, committed project file on every re-enable.

Flip the enabled key on the target file's own raw JSON via the existing LoadProjectRaw/SaveProjectRaw and LoadLocalRaw/SaveLocalRaw scoped accessors instead, preserving each file's other keys untouched. Merge semantics are kept for runtime reads (IsEnabled, etc.) — only the enable/disable write path changes.