Since 3fffeb1 prboom.wad is compiled into the core (d_main.c:1449-1465). The IWADs it searches beside the content, in system/prboom/ and in system/ are now listed, with the ZDoom pk3 loaded before a pk3 mod.
A file that arrives with the emulator is already on the user's machine
and the packs leave it out. 4558 collected copies (1.4 GB) were reached
only by such entries, with no platform, other profile entry or install
manifest needing them. They are removed, and two release-asset copies
leave the ignore list. bundled_only.py now lists every copy of a listed
file, since the database keeps one path per content, and pipeline step
4d fails while one remains.
100 emulator names the two platforms run had no profile, so their packs carried nothing for them. Each was read from the platform's own launcher or scriptmodule: the same program as an existing profile takes the name in cores:, a different build gets its own profile read from that version, a launcher or self-contained game goes to remove_cores, and the rest are new profiles written from their source or shipped binary. The files they need that the collection lacked are collected from the upstream distributions. Bungie and splitwolf trees are read by path and stay out of dedup.
VICE: basic, chargen, kernal for x64sdl libretro core.
QEMU: SeaBIOS 1.16.3 + VGA BIOS from system package.
PCem: MDA font ROM from PCem v17 ROM set.
Freedoom: freedoom1.wad + freedoom2.wad for prboom.
Commander X16: rom.bin R49 from x16-rom releases.
Apple IIGS: ROM01 from asimov mirrors.
DSi: NDS_Bios7i, NDS_Bios9i, DSi_Firmware, SGB_(JU).