D281 - Projects live under src/, and the encoder section finished its wiring

decided - 2026-09-01 (user-directed cleanup sweep)

Two things the D280 work left unfinished, done here.

The encoder section (106-encoder) is now fully wired. D280 added the section but skipped two of the five "before adding a check" steps, so mkmodule/verify.sh would have refused: the three libSceVencCore imports are now in src/probe/imports.c, and the names are in surface.txt's @called-elsewhere block (they were in no census group, so nothing to remove). make check is green with them.

Structure: every source project is under src/. They were scattered at the top level. Now src/ holds only project directories - probe/ (the conformance probe: what used to be the loose src/*.c plus src/sections/), injector/, porthole/, tracer/, experiments/ (the loose boot.c/hwreport.c bring-up sources), and the shared common/ (freestд, used by both probe and injector) and shaders/. The Makefile's source lists move to src/probe/…; its object machinery ($(patsubst src/%.c,…), the src/%.c pattern rules) needed no change because the % already absorbs a nested directory - obj/host/probe/sections/… is created the same way obj/host/sections/… was. src/common/ stays put precisely because it is shared, so it is not the probe's to own.

The move made the doccheck claims stale, which is a gate failure, not cosmetics. verify.sh's doccheck enforces  directives, and every one pointed at a moved file (src/crt.c, src/harness.c, src/sections/sync.c, src/net.c, src/net_posix.c). All were repointed to src/probe/…, along with the current-reference prose in CLAUDE.md, GNM.md, HARDWARE-PROBE.md, BACKLOG.md, INJECTOR.md and the two hardware scripts' default source paths. Historical DECISIONS/WORKLOG prose describing the old layout is left as the record it is.

Litter, in the same sweep: .gitignore gaps closed (*.pkg, obscene-report-*.txt, the vulkan cache, /stdout.txt), two tracked junk files removed, and the regenerable root artifacts deleted.