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/speckit.clarify.agent.md

@@ -62,7 +62,7 @@ Note: This clarification workflow is expected to run (and be completed) BEFORE i
 
 Execution steps:
 
-1. Run `.specify/scripts/powershell/check-prerequisites.ps1 -Json -PathsOnly` from repo root **once** (combined `--json --paths-only` mode / `-Json -PathsOnly`). Parse minimal JSON payload fields:
+1. Run `packages/casan-harness/scripts/powershell/check-prerequisites.ps1 -Json -PathsOnly` from repo root **once** (combined `--json --paths-only` mode / `-Json -PathsOnly`). Parse minimal JSON payload fields:
    - `FEATURE_DIR`
    - `FEATURE_SPEC`
    - (Optionally capture `IMPL_PLAN`, `TASKS` for future chained flows.)