Why don't I have a custom title by now?!
The WAD format is one thing that hasn't changed throughout Doom's development, so you can look at the alpha and see for yourself.
So, I guess I have a question regarding that. Before Doom was using binary space partitioning, did maps have to be "compiled" before they were run? From what I understand, some of the map lumps, namely SSECTORS, SEGS, and NODES, store a breakdown of the map geometry defined by LINEDEFS, SIDEDEFS, SECTORS, and VERTEXES. These are obviously related to the use of BSP. So before BSP, was Doom using another node format, none at all, or was it doing something similar to Wolfenstein?
In Alpha 02, the single map is comprised of the following lumps: M_AREA, M_FNAMES, M_LINES, M_PLANES, M_PNAMES, M_POINTS, M_TEXTUR and M_THINGS. I'd guess that M_AREA corresponds to SECTORS, M_LINES to LINEDEFS and M_POINTS to VERTEXES. M_FNAMES corresponds to a list of flat names, M_PNAMES to a list of patches. M_TEXTUR seems like it's an early version of the TEXTUREx lumps, but I haven't looked too deeply into it. Not sure what M_PLANES is meant to be.
Alpha 04 introduces multiple maps with a "header then lumps" structure closer to their eventual form. The lumps are FLATNAME, POINTS, LINES, SECTORS and THINGS. Alpha 05 is the same.
Then there is the turning point after that. When the press release beta is sent, the map lumps have reached their final state with just one exception: in the beta, the REJECT lump isn't there yet.