David Corley says:

Having set up exclusion rules, and seen them not work, I checked the forums to find Matt Watsons comment here:

http://forums.atlassian.com/thread.jspa?messageID=257335942&#257335942

I think the documentation needs to be updated to:

1. Break down the phases of the initial scan and explain what each phase is for (creating changeset,index,generating linecount ,etc.). It would be really useful to know what to expect.

2. Define which phase(s) actually apply the include/exclude rules. (it seems the "creating changesets" phase does not, but later phases do)