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Thanks for your requests/suggestions. I have added them to my TODO list and may implement them soon.
For merging PGN books it is easy. Actually you can merge them manually because they all are text files. BSG can do a bit better since it can filter out all double openings. However, what you say "one book has priority over the other" won't work since PGN books have no weights thus all openings are totally equal in term of priorities.
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I don't care about the book weights of a merged pgn book as I don't want to use the book for engine matches or to play against an engine.
I want to use the book merging option to filter out moves.
For example if I make a book only-white from a pgn with manually chosen opening lines and I merge this book with a book only-white from a big database with high quality games. Then the output would have only the white lines of the first book + white replies against the black moves if they are not in the first book.
Like described in following link under the title "Book Merging"
http://wbec-ridderkerk.nl/html/details1/PolyGlot.html
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If this is not possible, I would like to request some other way to achieve the same result. Say for example, I have two pgn books. 'Elo_2500_gg', (with all variations for white and for black); and 'Elo_2500_gg_mainlines', (with only the main lines for white and for black). Now I want to create a new pgn book, 'referense_white', to use as reference for my white repertoire. I want the book to include all lines for white from the book 'Elo_2500_gg_mainlines' and all lines for black from the book 'Elo_2500_gg'. I only want white reply’s from the book 'Elo_2500_gg' to be included in the book 'referense_white' if there is no white reply already included in the book 'Elo_2500_gg_mainlines', transpositions included. If there was an efficient way to convert bin books to pgn, I could already do this by using the book merging options of bin books. Maybe there is already some method to achieve this? With pgn-extract or maybe some others software.