Raw programming of an Altera FPGA
Surely if you were able to fully comprehend and become knowledgeable of all of the following factors regarding a particular FPGA it would be possible to hand craft programming files for the device.


Detailed binary format requirements for FPGA programming file.
Mapping of how programmable cell states of programming file map to features of the FPGA.
Detailed understanding of the protocol used to load a programming file into the FPGA.
Thorough understanding of the logic cell structure of the FPGA and how it maps to programmable cells.
Full comprehension of how internal routing functions work and how connectivity is related to programmable cells.
Good knowledge of how the I/O cells work and how they bus into the interconnect matrix of the FPGA.
Understanding clocking requirements of the FPGA and how this relates to power on initialization.
Detailed understanding of how the global clock distribution network in the FPGA is routed and connected to other internal elements.
Good comprehension of the global reset domains of the FPGA and how they are routed and connected to internal elements.
An understanding of how hard coded macro cells of the FPGA work including repeaters, buffer memory, PLL, DPLL, SERDES and any other things the manufacturer has chosen to throw into the mixing pot.


I have probably left out a basket full of additional details that would be very important to be familiar with that would play into making successful hand coded designs. Timing and delay compensation come to mind here.

It should become obvious very quickly that there is a reason that FPGA vendors provide development tools to cover almost all of these details. Using a recognized standard description language to describe the function intended for an FPGA design makes your intellectual property portable to almost any FPGA. Trying to understand what you have asked about regarding hand crafting a programming file is easily 20 to 30 times the work and would only be usable on one or two devices in some specific FPGA family. I suggest that your energy would be much more well spent becoming an expert at usage of the standardized description language.

If part of your curiosity is a drive toward becoming a designer/creator of FPGA components themselves then I suggest that you start by focusing on one particular aspect of the technology and learn that. If you had a job at one of the FPGA houses you would be part of a large team that includes dozens of skillsets that all come together to produce the FPGA products and tools that you will find in the market today.