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>

.claude/agents/okr.srsallsystem.md

@@ -39,7 +39,7 @@ Mission: produce a **complete, exhaustive, system-wide SRS** covering all module
 
 If `$ARGUMENTS` specifies a file or folder path, **read that path first** as the primary source. Otherwise, read in this priority order and cross-reference:
 
-1. **`docs/input/okr-requirement.md`** — Original product requirement document. **Primary source of truth.** Contains functional requirements, screen definitions, field rules, user flows, and validation constraints.
+1. **`apps/okr/domain/input/okr-requirement.md`** — Original product requirement document. **Primary source of truth.** Contains functional requirements, screen definitions, field rules, user flows, and validation constraints.
 2. **`docs/technical_architecture.md`** — Technology stack recommendations. Use for the technology recommendation section only (not for functional requirements).
 
 **Priority rule:** User-specified input (`$ARGUMENTS`) → Special Specification (Spec) → system-overview.md → `[TBC-XX]` if all are insufficient.