UPDATE: This is generally correct, but it has been superseded by this.
So when we open them in the future, they cause as little trouble as possible.
Everything in the drawing should be moved to one of two layers: '+A Arch Note Reg Scale' and '+A Misc Line'.
When you merge geometry, layers in the merged data which don't exist in the project get created. Fewer layers means fewer surprise-new layers when merging. These layers are not only annoying, they are dangerous. Remember that new layers are hidden in all LCs. That means the drawing you think you're using is hidden. Cool! Not.
You should also purge the unused attributes using attribute manager.
Once you have saved the module, open it.
Everything in the drawing itself goes to +A Misc Line. All of the notes go to +A Arch Note Reg Scale. The notes are: Text blocks, leaders, level dimension markers, dimensions, note symbols such as roof slope markers, and the drawing title.
The easy way: Select everything. Use Edit Selection Set to change the layer to +A Misc Line. Use the arrow tool to box the note column, including the level dimensions and the leaders. Shift-click on the other note elements. Use Edit Selection Set to change the layer to +A Arch Note Reg Scale.
Open the attribute manager with Cmd+Opt+Ctrl+A (Options | Attribute Manager). Click the 'All' tab. In the lower left, click the Purge Unused button, then 'Apply', then OK all the boxes.
Save the module and move on.