The latest calibre release (0.9.19) has a new feature
"Polish Books". To use it go to Preferences->Toolbars and add the Polish Books action to the main toolbar, then select the books you want polished and click "Polish books".
Quote:
Polishing books is all about putting the shine of perfection onto your carefully crafted ebooks.
Polishing tries to minimize the changes to the internal code of your ebook. Unlike conversion, it does not flatten CSS, rename files, change font sizes, adjust margins, etc. Every action performs only the minimum set of changes needed for the desired effect.
You should use this tool as the last step in your ebook creation process.
Note that polishing only works on files in the AZW3 or EPUB formats.
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Currently the operations you can perform are:
Subsetting embedded fonts
Subsetting fonts means reducing an embedded font to contain only the characters used from that font in the book. This greatly reduces the size of the font files (halving the font file sizes is common). For example, if the book uses a specific font for headers, then subsetting will reduce that font to contain only the characters present in the actual headers in the book. Or if the book embeds the bold and italic versions of a font, but bold and italic text is relatively rare, or absent altogether, then the bold and italic fonts can either be reduced to only a few characters or completely removed. The only downside to subsetting fonts is that if, at a later date you decide to add more text to your books, the newly added text might not be covered by the subset font.
Updating metadata
This will update the metadata and covers in the book files to match the current metadata in the calibre library.
When updating covers in epub files that do not have a correctly identified cover, it will insert a new cover at the start of the book.
Adding/removing metadata jackets
It can add or remove metadata jackets from the ebook files. A metadata jacket is a page at the begining of the book that lists all the book's metadata: title/authors/series/ratings/tags/comments etc.
Note that this feature is based on a completely new codebase, so there may be bugs.
You can also use it from the command line:
http://manual.calibre-ebook.com/cli/ebook-polish.html