docs: align all documentation with the new repo structure

Update agent protocols (.claude/agents, .github/agents), guides, runbooks and READMEs
to the post-restructure layout: .specify/{scripts,tests,security,config,templates,
governance,memory,level5-config} -> packages/casan-harness/...; docs/input +
golden-runs + traceability-map -> apps/okr/domain/...; drop AINative_OKR_CASAN5/ prefix.
Runtime-state paths (.specify/logs, .specify/agentops, .specify/level5/central-governance)
kept as-is. Historical evidence under docs/output/ left untouched (immutable run records).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

.github/agents/protocols/pipeline-context.md

@@ -32,22 +32,22 @@ tech-stack:
 casan-harness:
   level-target: 5
   h4-security:
-    policy: .specify/security/prompt-filter.yaml
-    output-policy: .specify/security/output-policy.yaml
+    policy: packages/casan-harness/security/prompt-filter.yaml
+    output-policy: packages/casan-harness/security/output-policy.yaml
     audit-log: .specify/logs/audit/security.jsonl
   h5-governance:
-    approval-flow: .specify/governance/approval-flow.yaml
-    risk-registry: .specify/governance/risk-registry.yaml
+    approval-flow: packages/casan-harness/governance/approval-flow.yaml
+    risk-registry: packages/casan-harness/governance/risk-registry.yaml
     audit-log: .specify/logs/audit/audit.jsonl
   h6-agentops:
     metrics-policy: .specify/agentops/metrics.yaml
     metrics-log: .specify/logs/cost/metrics.jsonl
     alert-log: .specify/agentops/alerts.log
   h2-tool-registry:
-    registry: .specify/level5/tool-registry.yaml
+    registry: packages/casan-harness/level5/tool-registry.yaml
     audit-log: .specify/logs/level5/tool-registry.jsonl
   h7-drift:
-    golden-dir: .specify/level5/golden-runs/
+    golden-dir: apps/okr/domain/golden-runs/
     drift-log: .specify/logs/level5/drift.jsonl
   rollback:
     transactions-log: .specify/logs/level5/rollback-transactions.jsonl