Add clean key on scan to control whether scanned directories are removed

If collector invokes a scan operation on a worktree, it will currently remove any directories it scans. The assumption is that these directories were created by the run command. However, there are situations when this cleanup is not desirable, such as if collector is being used to scan directories managed by a separate tool or if the directories are somewhere else in the project's worktree. By default, the scan operation should not clean the directories it scans. The behavior would have to be activated by the user by setting the clean: true key in the scan configuration.