Quote:
Originally Posted by kensmosis
I won't have to monkey about with the db directly!
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kensmosis - Not only won't you have to, but if you were to do so you would be opening up a Pandora's Box full of mare's nests and snake pits

In other words - don't even think about tinkering with the metadata.db file in the library directory.
That said examining the structure with something like SQLite Browser can be very informative, and browsing tables is sometimes necessary - eg to get an author's id to use in a 'canned' content server query.
Regarding rest of the library i.e. the author and book folders, the rules are simple - don't add any subdirectories or files, don't change the names of subdirectories or files, and don't delete or move any subdirectories or files.
But, let's say you open a TXT format in, let's say OOo Writer via Calibres View->Open With feature, and you use Writer to add Chapter Headings and such, and then save it as DOCX. By default it will be saved to the book folder - that's OK, open the Book folder by tapping 'O', and then drag and drop the DOCX into the Book details sidebar (normally on the right).
There are occasions when you may want to edit a format file directly rather than via calibres View options - e.g. to replace a crappy cover image in an existing cbz via an archive utility.
Just be mindful of what you're doing.
BR