With one of the latest versions (I'm not sure which as I don't update every cycle, but the first time I saw it was with 3.38) calibredb has stopped adding covers specified in .opf files when you add using --one-book-per-directory.
I have a routine that places a PDF in a directory, creates an .opf file for it, creates a .jpg cover then calls calibredb, and the cover is no longer set, instead you get the blue default cover, in previous versions the cover was added correctly.
When I add from the front end interface using the the One book per directory option, the cover gets added correctly, but not when using calibredb.
To make sure it wasn't something in my .opf file, I just created a new blank library, manually added a pdf, set the author/title and cover for the pdf and saved that book to disk from calibre (S) and moved the resulting book directory to d:\cdbtest. Then removed that book from the library and tried re-adding it using calibredb.
Code:
C:>"c:\Program Files\Calibre2\calibredb.exe" --with-library=http://localhost:8080/#Testing add --one-book-per-directory "d:\cdbtest"
Added book ids: 2
The book adds with the correct Author/Title, but with
No Cover.
I ran this test with version 3.39.1 [64bit]