Other problems include non-deterministic filesystem order, randomized hash algorithms, and even the fact that Markdown processors mangle email addresses randomly. A highly vexing problem that I'm currently trying to solve is that libxslt implements the XSLT generate-id() function by taking the memory address of the XML node struct, which makes documentation generated with XSLT non-reproducible (memory addresses are non-deterministic because of address space randomization and randomized hash tables).
(I'm the author of strip-nondeterminism, a tool in our custom toolchain that attempts to normalize files after they're built.)