organize: add optional `--disappeared=error|remove` or `--mode=complete|incremental`

If `organize` is (re)run on a full collection of files, some of which were modified, then by "injecting" new files and leaving previously organized ones we might end up breeding some . With something like `--disappeared` we could detect which paths were no longer considered and offer to remove them.

Alternatively - we could make a default mode to be "complete" (default) which would imply removing files which were not "re-organized" (probably should ask first since could lead to the loss of data) and only by adding explicit `--mode=incremental` (complete - default) new file added in, while allowing all previous stick around.

Start at the `organize` command entry point and trace how it identifies files that are re-organized versus previously organized. The issue presents two competing interfaces, so first establish whether `--disappeared` or `--mode` is wanted and how removal should be confirmed. Done means the selected behavior is specified, implemented, and covered for complete and incremental runs.

Written by the indexing model from the issue text.