I completely agree. It is a year after the original posting and I am having this same issue. We used the arduino to make a simple temperature control unit, and want to "solidify" the build so we can generate the same hex file from source sometime down the line. Which would mean "freezing" the versions of all the include files and saving the toolchain used for the compile. The dynamic updating of the Arduino IDE and libraries is great for hobby use, but makes it hard to get serious.
I've located makefiles via Google search, but they are for the MacOS or Linux. I'm working on Windows and haven't found a walkthrough for a windows setup. A makefile would make life much simpler.