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/prompts/demo-promt.md

@@ -2,7 +2,7 @@
 ## step 1: gen wide system srs
  - use agent: 　okr.srsallsystem
  - Prompt
-> Generate system-wide SRS (Full Module Requirements Definition) for the OKR web app base on input at docs/input/okr-requirement.md
+> Generate system-wide SRS (Full Module Requirements Definition) for the OKR web app base on input at apps/okr/domain/input/okr-requirement.md
 
 ## step 2: chọn module sẽ tạo
 ### a. Case run from vscode
@@ -18,4 +18,4 @@
 # II. Change spec
 ## step 3: thực hiện CR cho 1 module
  - Prompt
-> execute an UPDATE pipeline for change requests at docs/input/change-request/change-0405.md for MOD-02: Workspace & Dashboard
+> execute an UPDATE pipeline for change requests at apps/okr/domain/input/change-request/change-0405.md for MOD-02: Workspace & Dashboard