docs(P00): research v0.9 re-architecture — codebase audit + prior-context review

Reconciles the PRD against the shipped v0.8 codebase. Audit confirms the
PRD's R-series and D-068+ describe a re-architecture (not a continuation):
6 foundational axes contradict the shipped code (daemon, transport, CA,
identity, config format, namespace model) and 8 subsystems are net-new.
Prior planning corpus (IDEATION/GRILL/RESEARCH v0.2-v0.8) confirmed no
v0.9/v1.0 plan existed; step-ca was explicitly rejected (AD-010); SPIFFE
was rejected (PROJECT.md:94). The re-architecture is the first direction
change in the project's history.

---ci---
project: orca
phase: 0
milestone: v0.9
status: research
---/ci---

.ciagent/CHECKPOINT.json

@@ -1,11 +1,11 @@
 {
   "phase": 0,
-  "stage": "specify",
+  "stage": "research",
   "milestone": "v0.9",
   "milestone_slug": "rearchitecture",
   "phase_role": "pre_execution",
   "attempts": 0,
-  "updated_at": "2026-08-05T02:00:00Z",
+  "updated_at": "2026-08-05T02:05:00Z",
   "milestone_complete": false,
   "next_milestone": null
 }