I just upgraded to doxygen from jessie (1.8.8), and when I got SqLite3-related errors as mentioned above, I tried 1.8.9.1 from testing, which also gave those errors. After consulting with Dimitri van Heesch (author of Doxygen), it turns out that SqLite3 support is still a work in progress & should therefore not be enabled at compile-time for Debian. When I downloaded Doxygen-1.8.9.1 binaries for Linux/x86_64 from http://www.stack.nl/~dimitri/doxygen/download.html, sure enough I found my documentation builds without these errors, and no doxygen_sqlite3.db file is left behind by doxygen. I'll continue using that version of Doxygen until Debian's doxygen is fixed.
