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Import a large source tree into a project. Close the project. Open the project. Notice that files that do get included from other files still get indexed separately. What I would suggest is doing it in 2 passes : first doing all the cpp/cc files, then doing the extraneous headers that aren't in your list. Otherwise, you have to update the index job with info about which files it can remove from its list.
Fixed in head and stream as of August 19th. - B