@Steven:
Here are my proposal for improving this feature regarding those "bugs" I reported. All cases under assume auto-organization is enabled.
1. When the user is trying to move the location for auto-organization to another drive, currently MB shows a warning that those files on the old location won't move to the new drive. If the user forces it, then those files remain in the old drive but still remain in library too without being auto-organized any more.
Offer following options for those files: (1) Send to inbox (default), (2) Move files, (3) Copy files.
2. When "add to inbox" is ticked for new files action, do not allow to use the same location as the one for auto-organization. Currently this results to files co-residing both in library and in inbox.
3. When "add to library" is ticked for new files action, disable auto-sweep option. For auto-organized library, this setting is bound to cause a conflict.