Scan a lot or a little
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There are two main ways to control how much of your drive BC looks at.
When you collapse the folder tree in Beyond Compare, it will stop comparing things. And the statistics at the bottom of the screen will only tally up the files that are showing in the open view.
When you expand the entire tree, BC will scan, align, and compare everything.
In the menu:Tools->Options->Handling->AutomaticallyScanFoldersInTheBackground
This will prevent scanning on closed folders
