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/okr.bossbuiltin.agent.md

@@ -115,10 +115,10 @@ report-nn: <NN>           # for speckit.implement only
 report-phase: <phase>     # for speckit.implement only
 casan-harness:
   required: true
-  h4-security: ".specify/scripts/bash/security-check.sh"
-  h5-governance: ".specify/scripts/bash/governance-check.sh"
-  h6-agentops: ".specify/scripts/bash/agent-metrics.sh"
-  wrapper: ".specify/scripts/bash/casan-harness.sh"
+  h4-security: "packages/casan-harness/scripts/bash/security-check.sh"
+  h5-governance: "packages/casan-harness/scripts/bash/governance-check.sh"
+  h6-agentops: "packages/casan-harness/scripts/bash/agent-metrics.sh"
+  wrapper: "packages/casan-harness/scripts/bash/casan-harness.sh"
   evidence:
     trace-dir: ".specify/logs/trace"
     audit-log: ".specify/logs/audit/audit.jsonl"