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- Drop the superseded docs/PLAN-linear-level-sweep.md.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.

tools_pc/d88_emit.py

@@ -51,7 +51,7 @@ the cumulative shift from growth ahead of them in the file):
     KNOWN BUG (D125, unfixed as of M-13): the converted blob does not land
     correctly in the emitted file for some levels (Aztec/Bunker2/Surface2) --
     suspect the pass-1 delta / region-`end` handling here (~L308-340), NOT
-    convert_stream itself. See internals.md D125 + docs/LEVEL-STATUS.md.
+    convert_stream itself. See internals.md D125 + docs/dev/LEVEL-STATUS.md.
   - waypoint.neighbours / waygroup.neighbours / waygroup.waypoints /
     PathRecord.waypoints target arrays: plain `s32` ID lists (NOT file
     offsets -- graph node indices), NULL/-1 terminated, walked with real