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Search will search the entire card, regardless of the view you are in when you click Search.
As Shaggy points out, I explained how the tagging works in one of my other posts. The hypothesis is correct: every PDF or EPUB document that is not inside one of the special folders (News, Images, Personal Documents, Help) is tagged as a book. You can edit the 'global.db' SQLite3 database to change the tag. But that is experimental.
The idea is that you put all your personal documents (not being books) inside the 'Personal Documents' folder. Once the sources are released, it will be trivial to change the 'Personal Documents' to use folder-based browsing.
If you want a file to be excluded from indexing you can put it somewhere inside the 'System' folder, but then it will not be accessible at all (also not through the SD Card view). Also, you can make hidden files and folders by starting the name with a dot or an underscore. These will also not be indexed (and therefore also not be accessible).
Hope that helps.
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