MLton and SML/NJ take different inputs to drive their build processes. The main Makefile is responsible for building src/domtool.cm (the input to SML/NJ) and src/domtool-*.mlb (the tool-specific inputs to MLton) from src/sources and some other compiler-specific files. When adding a new source file to the system, include it in src/sources, not any of the generated files, and take care to insert it in dependency order relative to the sources already in the file.
A C library openssl_sml.so is built to provide a cleaner (but spartan) interface to the OpenSSL library. The Makefile uses the NLFFI tools shipped with MLton and SML/NJ to build compiler-specific SML interfaces to this library, and then compiler-agnostic code takes over and defines the visible OpenSSL structure based on the common interface supported by all NLFFI tools. Code specific to compiler $COMPILER lives in domtool2/openssl/$COMPILER.