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yes searching ignores markup.
No not really. Annotations are not large amounts of text, so putting them into the main database is harmless and they are per book so they integrate with the backup schema of OPF files very well.
You cant have search via the main bar. The main bar searches for books. Here we are searching for categories such as an author/tag. There will be a dedicated browse notes tool just as there is for annotations that will use the FTS data.
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