docs: add operating manual, fix cross-references after doc restructure

- Commit CLAUDE.md + AGENTS.md so a fresh clone has the operating manual and
  the ABI/no-game-logic rules (trimmed of stale phase status; the personal
  pd_port path removed; points at the split docs).
- Sweep every stale doc reference across the tree after the restructure:
  PCPortResearch.md -> internals.md / dev/findings.md,
  PORT-LEARNINGS.md -> porting-notes.md,
  AGENT-WORKFLOW.md -> dev-process.md,
  docs/{GRAPHICS-BACKLOG,HANDOFF-ARCHIVE,GE-ENV-PROBES,LEVEL-*,TEXTURE-GLITCH-ANALYSIS,AUDIT-M6-*,AUDIO-PLAN}.md -> docs/dev/.
- Drop the superseded docs/PLAN-linear-level-sweep.md.
- docs/HANDOFF.md + docs/BACKLOG.md stay local-only (rolling working files);
  CLAUDE.md now handles their absence in a fresh clone.

AGENTS.md

@@ -0,0 +1,61 @@
+# AGENTS.md — GoldenEye 007 PC Port
+
+## What this is
+
+- `n64decomp/007`: WIP decompilation of GoldenEye 007 (N64), byte-matches US/EU/JP ROMs.
+- Active work: **PC port** modelled on the Perfect Dark PC port (same Rare "Indy" engine family).
+- **Reference docs:** `docs/internals.md` — architecture, GE-specific RSP deltas, phased plan (§1–§10). `docs/dev/findings.md` — the `Dxx` finding log (§F + §H, indexed at the top of §F); read the entry you need, don't linear-read. `docs/porting-notes.md` — the recurring N64→PC bug classes, one screen.
+- **Current status:** the README "Status" section. Current task + environment: `docs/HANDOFF.md` (a rolling local working file).
+- **Dispatching subagents?** `docs/dev-process.md` — task budgets/deadlines, file partitioning, pre-flight, the standard brief template. Every investigation subagent reads `docs/porting-notes.md` first and appends to it.
+
+## Non-negotiables
+
+1. **N64 build untouched.** `Makefile`, `tools/`, `rsp/`, `ld/` belong to the N64 build. Never modify them for the PC port.
+2. **Game logic is unmodified.** The decomp's control flow and behavior are ground truth for 1:1 fidelity — never change them. All N64 *hardware* dependencies are satisfied by the `port/` layer; if a game file seems to need a behavioral change, stop — the fix belongs in `port/`. **Narrow exception (ABI/layout only):** the 32→64-bit transition forces a small class of mechanical, semantics-preserving edits that cannot be isolated in `port/` — chiefly pointer-width reconciliation in ROM-serialized structs (a struct with a 32-bit-pointer field misaligns when read as 64-bit). These follow the PD ground-truth pattern (store the embedded address as `u32`, cast to a real pointer at the use site), change no logic or behavior, and are each documented in `docs/dev/findings.md` §F/D3x. No other game-code edits are permitted.
+3. **Region macros mirror the Makefile.** `CMakeLists.txt` `REGION_DEFS` must match the N64 Makefile's per-region macro set exactly (finding A1). Divergence = silent branch divergence + link failures.
+4. **`src/libultrare/Makefile.libultrare` is ground truth** for original-vs-Rare libultra files (finding B3). The PC build compiles: `libultra/audio`, `libultrare/audio` (drvrNew/env/reverb), `libultra/gu`, and `libultrare/io/vitbl.c` only. All other `io/` + `os/` files are excluded and shimmed in `port/src/libultra.c`.
+5. **`rsp/graphics/gmain.s` is the RSP ground truth** — the authoritative reference for which GBI commands GE emits (modified fast3d, 1545 lines). We do not run it on PC; `port/fast3d/` replaces it. Use it to validate the software RSP's command decoding and the custom CC/RM modes.
+
+## Critical files
+
+| File | Role |
+|---|---|
+| `docs/internals.md` | Architecture + RSP deltas + phased plan (§1–§10). Reference, not a linear read. |
+| `docs/dev/findings.md` | The `Dxx` finding log (§F/§H, indexed at top of §F). |
+| `CMakeLists.txt` | PC build (parallel to the N64 Makefile). Source list + `REGION_DEFS` live here. |
+| `port/src/` | Shims: `libultra.c` (OS API), `gesched.c` (scheduler), `n64stubs.c` (boot/TLB/FPU/rmon), `random.c` (PRNG ported verbatim from `random.s`), `ucode.c` (microcode segment markers), `main.c`, `video.c`, … |
+| `port/fast3d/` | Software RSP (adapted from the PD port). The main Phase 2 work. |
+| `rsp/graphics/gmain.s` | GE's RSP ucode — ground truth for GBI/CC/RM. |
+| A local **Perfect Dark PC port** checkout ([fgsfdsfgs/perfect_dark](https://github.com/fgsfdsfgs/perfect_dark)) | **Standing reference** — consult it whenever a work item has a PD analogue (same Rare engine family): port-layer ground truth (`port/fast3d/`, crash/system/video), plus copy candidates `port/src/preprocess/` (N64→PC asset conversion; `filemodel.c` is the D43 near-analogue) and `mixer.c`/`input.c`/`fs.c`. Port-layer files only; same family ≠ identical format — validate per field. Full audit: `docs/internals.md` §2.4. |
+
+## Build
+
+```sh
+./build-pc.sh ntsc-final   # or pal-final / jpn-final
+```
+
+Needs CMake + SDL2 + zlib + OpenGL, and must run from the MSYS2 MINGW64 shell
+(see `build-pc.sh` header and `docs/building.md`). ROM goes in `./data/`
+(not distributed); assets must be extracted from it first (`docs/building.md`).
+
+## Verification ritual (after any build-affecting change)
+
+1. **Undefined symbols.** Every symbol referenced by the compiled set (see `CMakeLists.txt`: `SRC_GAME`, `SRC_ENGINE`, `SRC_LIBAUDIO`, `SRC_LIBULTRARE_AUDIO`, `SRC_LIBULTRARE_DATA`, `SRC_GU`, `SRC_PORT*`) must be defined exactly once in the compiled set or in `port/`. Symbols that live in EXCLUDED files (`libultra/io/*`, `libultrare/io/*` except `vitbl.c`, `libultra/os/*`, `libultrare/os/*`, `sched.c`, `rmon.c`, `vi.c`, `src/*.s`) must be provided by `port/src/libultra.c`, `gesched.c`, `n64stubs.c`, `random.c`, or `ucode.c`.
+2. **Duplicates.** No symbol defined twice across the compiled set (watch `sp_*` stacks, `rmon*`, `os*` shims, segment markers).
+3. **Syntax.** Every touched file must parse; `./build-pc.sh` is the final word.
+
+Run `/linkcheck` for this sweep. Record new findings in `docs/dev/findings.md` §F/§H style (next `Dxx` label after the last used) and add the label to the §F index.
+
+## Phase status (summary — see README + `docs/dev/findings.md` for detail)
+
+- **Phase 0–1.5:** done. Build system, boot chain, OS-shim layer, fast3d
+  integration, first frames, full intro rendering.
+- **Phase 2 (rendering):** in progress. All 21 solo levels load + render +
+  survive an unattended window; front end (menu → mission select → briefing →
+  start) is functional; file-backed EEPROM saves work. Cosmetic defects are
+  parked in `docs/dev/GRAPHICS-BACKLOG.md`.
+- **Phase 3 (audio + input):** input layer done (`port/src/input.c`); polish
+  bugs open (D118*, D169). Audio not started — libaudio → SDL, copy-and-adapt
+  from the PD port's `mixer.c`.
+- **Phase 4 (saves + polish):** file-backed EEPROM done; widescreen, config,
+  rebinding UI outstanding.