What's the 'Clean up' button for'

The ‘Clean up’ button only works in Index.

Is it necessary to place on upper side of main windows?
or is there other usage?

I’m not sure what you mean by “only works in Index”—perhaps you meant “Inbox”? Regardless, “Clean Up” removes from view all the items that you have checked off as completed. In OF v2 beta it works in Project view and Forecast view. (It may work in the other views, but I haven’t tested it. Certainly, it worked that way in OF v1).

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Thank you! I meant “Inbox” and while I did not complete any task yet so I really dont know how can I use this function at other view mode.

command + K also does it.

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In the Preferences you may specify when to move tasks out of the inbox and which tasks to move.

when: “Clean up changed items: immediately OR when changing views”
which: “Clean up inbox items which have: a context/a project/both/either”

Clean Up is the manual version.

Depending on your preferences, you may be in any view when setting contexts and projects and then want to force a clean up without changing views.