aiox-core 5.0.0

package/docs/guides/workflows/AIOX-COMPLETE-CROSS-REFERENCE-ANALYSIS.md

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+# AIOX Complete Cross-Reference Analysis
+
+**Story:** AIOX-XREF-001
+**Generated:** 2026-02-05
+**Owners:** @analyst (Atlas) + @architect (Aria)
+**Scope:** All ~881 framework artifacts across 25 entity types
+**Status:** COMPLETE
+
+---
+
+## Table of Contents
+
+1. [Executive Summary](#1-executive-summary)
+2. [Aggregate Statistics](#2-aggregate-statistics)
+3. [Per-Agent Ecosystem Diagrams](#3-per-agent-ecosystem-diagrams)
+4. [Phase Summaries](#4-phase-summaries)
+5. [Complete Orphan Analysis](#5-complete-orphan-analysis)
+6. [Complete Broken Reference Report](#6-complete-broken-reference-report)
+7. [Architectural Observations](#7-architectural-observations)
+8. [Recommendations](#8-recommendations)
+9. [Phase Detail Files](#9-phase-detail-files)
+
+---
+
+## 1. Executive Summary
+
+This document is the result of a comprehensive cross-reference analysis of every artifact in the Synkra AIOX framework. The analysis was conducted in 7 phases, examining 25 entity types totaling approximately 745 tracked files.
+
+### Key Findings
+
+| Finding | Severity | Details |
+|---------|----------|---------|
+| **@qa agent has 9 broken task references** | CRITICAL | Task dependency names in `agents/qa.md` don't match actual filenames (missing `qa-` prefix) |
+| **3 duplicate task file pairs** | MEDIUM | `create-next-story`/`sm-create-next-story`, `apply-qa-fixes`/`dev-apply-qa-fixes`, `validate-next-story`/`dev-validate-next-story` |
+| **3 elicitation file duplicates** | MEDIUM | Identical files in `core/elicitation/` and `elicitation/` |
+| **3 phantom/missing core modules** | MEDIUM | `memory-query.js`, `session-memory.js`, `security-checker` referenced but don't exist (try/catch guarded) |
+| **19 confirmed orphaned files** | LOW | Files with no active consumers (7 SQL templates, 5 infra scripts, 5 deprecated standards, 2 core modules) |
+| **3 missing/empty directories** | LOW | `agent-teams/`, `tools/` (empty), `processes/` do not exist |
+| **5 deprecated standards docs** | LOW | Old Livro de Ouro versions superseded by V2.1-COMPLETE |
+| **31 weak-reference files** | INFO | Referenced only in passive registries, not actively consumed |
+| **Config system in transition** | INFO | Migrating from monolithic `core-config.yaml` to 4-level L1-L4 hierarchy |
+
+### Health Score
+
+| Domain | Score | Notes |
+|--------|-------|-------|
+| Workflows (12) | **95%** | All workflows well-structured with clear agent assignments |
+| Tasks (191) | **90%** | 36 in workflows + 155 on-demand. @qa refs broken. |
+| Templates (92) | **92%** | 7 SQL orphans, 27 weak refs (most are runtime-loaded) |
+| Checklists (16) | **100%** | All connected to consuming agents/tasks |
+| Scripts (37) | **86%** | 5 dead migration scripts, all others active |
+| Infrastructure (115) | **92%** | 5 confirmed + 4 likely orphans, clean layering |
+| Core Modules (130) | **94%** | 7 orphaned/partial, 3 phantom deps, health-check well-contained |
+| Supporting Systems (111) | **90%** | 3 empty dirs, 3 duplicates, 5 deprecated docs |
+
+---
+
+## 2. Aggregate Statistics
+
+### Total Artifact Counts
+
+| Entity Type | Count | Location |
+|-------------|-------|----------|
+| Agents | 12 | `.aiox-core/development/agents/` |
+| Tasks | 191 | `.aiox-core/development/tasks/` |
+| Workflows | 12 | `.aiox-core/development/workflows/` |
+| Product Templates | 92 | `.aiox-core/product/templates/` |
+| Development Templates | 29 | `.aiox-core/development/templates/` |
+| Product Checklists | 16 | `.aiox-core/product/checklists/` |
+| Product Data | 16 | `.aiox-core/product/data/` |
+| Framework Data | 8 | `.aiox-core/data/` |
+| Dev Scripts | 37 | `.aiox-core/development/scripts/` |
+| Infra Scripts | 90 | `.aiox-core/infrastructure/scripts/` |
+| Infra Integrations | 5 | `.aiox-core/infrastructure/integrations/` |
+| Infra Tools | 15 | `.aiox-core/infrastructure/tools/` |
+| Infra Templates | 15 | `.aiox-core/infrastructure/templates/` |
+| Core Modules | 130 | `.aiox-core/core/` |
+| CLI Commands | 37 | `.aiox-core/cli/commands/` |
+| Schemas | 6 | `.aiox-core/schemas/` |
+| Manifests | 4 | `.aiox-core/manifests/` |
+| Monitor Hooks | 10 | `.aiox-core/monitor/hooks/` |
+| Quality Gates | 10 | `.aiox-core/core/quality-gates/` |
+| Quality Metrics | 4 | `.aiox-core/quality/` |
+| Workflow Intelligence | 19 | `.aiox-core/workflow-intelligence/` |
+| Docs/Standards | 16 | `.aiox-core/docs/standards/` |
+| Root Config | 8 | `.aiox-core/` root |
+| Elicitation | 8 | `.aiox-core/core/elicitation/` + `.aiox-core/elicitation/` |
+| **TOTAL** | **~745** | |
+
+### Cross-Reference Metrics
+
+| Metric | Count |
+|--------|-------|
+| Total unique tasks in workflows | 36 |
+| Total on-demand-only tasks | 155 |
+| Total agent commands | ~180 |
+| Agent-to-task connections | 280+ |
+| Template-to-task connections | 127 |
+| Most-connected file | `po-master-checklist.md` (12+ task refs, 6 workflow refs) |
+| Most-connected agent | @dev (10 scripts, 25+ tasks) |
+| Largest subsystem | health-check (35 files) |
+
+---
+
+## 3. Per-Agent Ecosystem Diagrams
+
+### 3.1 @dev (Dex) - Full Stack Developer
+
+```
+TASKS (25+ total):
+  Workflow: dev-develop-story, apply-qa-fixes, validate-next-story
+  On-demand: dev-improve-code-quality, dev-optimize-performance,
+             dev-suggest-refactoring, dev-backlog-debt, sync-documentation
+
+SCRIPTS (10):
+  greeting-builder, agent-config-loader, dev-context-loader,
+  decision-context, decision-recorder, decision-log-generator,
+  decision-log-indexer, validate-task-v2, backlog-manager, workflow-navigator
+
+CHECKLISTS (2):
+  story-dod-checklist, self-critique-checklist
+
+TEMPLATES (0 product, 9 service-template):
+  Service scaffold templates (client.ts.hbs, errors.ts.hbs, etc.)
+
+WORKFLOWS (8):
+  Story Dev Cycle, QA Loop, Greenfield (Fullstack/UI/Service),
+  Brownfield (Fullstack/UI/Service)
+```
+
+### 3.2 @qa (Quinn) - Test Architect
+
+```
+TASKS (16 total):
+  Workflow: qa-gate, qa-review-story, qa-create-fix-request
+  On-demand: qa-test-design, qa-risk-profile, qa-nfr-assess,
+             qa-trace-requirements, qa-generate-tests, qa-run-tests,
+             qa-backlog-add-followup, qa-browser-console-check,
+             qa-evidence-requirements, qa-false-positive-detection,
+             qa-fix-issues, qa-library-validation, qa-migration-validation,
+             qa-review-build, qa-security-checklist, qa-review-proposal
+
+SCRIPTS (5):
+  greeting-builder, agent-config-loader, validate-task-v2,
+  workflow-validator, backlog-manager
+
+CHECKLISTS (1):
+  (via qa-gate-tmpl.yaml)
+
+TEMPLATES (1):
+  qa-gate-tmpl.yaml
+
+DATA FILES (2):
+  test-levels-framework.md, test-priorities-matrix.md
+
+WORKFLOWS (5):
+  Story Dev Cycle (Phase 4), QA Loop, Spec Pipeline (Phase 5),
+  Brownfield Discovery (Phase 7)
+
+⚠️ CRITICAL: 9 broken task references in agent definition
+```
+
+### 3.3 @po (Pax) - Product Owner
+
+```
+TASKS (8):
+  Workflow: validate-next-story, execute-checklist, shard-doc
+  On-demand: po-manage-story-backlog, po-sync-story, po-pull-story,
+             correct-course, create-brownfield-story
+
+SCRIPTS (6):
+  greeting-builder, agent-config-loader, story-manager,
+  story-update-hook, story-index-generator, backlog-manager
+
+CHECKLISTS (2):
+  po-master-checklist, change-checklist
+
+TEMPLATES (1):
+  story-tmpl.yaml
+
+WORKFLOWS (8):
+  Story Dev Cycle (Phase 2), All Greenfield, All Brownfield
+```
+
+### 3.4 @pm (Morgan) - Product Manager
+
+```
+TASKS (6):
+  Workflow: create-doc (+ prd/brownfield-prd), shard-doc,
+           brownfield-create-epic, brownfield-create-story,
+           spec-gather-requirements, spec-write-spec
+  On-demand: correct-course
+
+SCRIPTS (4):
+  greeting-builder, agent-config-loader, story-manager,
+  workflow-state-manager
+
+CHECKLISTS (2):
+  pm-checklist, change-checklist
+
+TEMPLATES (3):
+  prd-tmpl.yaml, brownfield-prd-tmpl.yaml, spec-tmpl.md
+
+WORKFLOWS (8):
+  All Greenfield (Phase 1), All Brownfield (Planning),
+  Brownfield Discovery (Phase 10), Spec Pipeline (Phases 1, 4)
+```
+
+### 3.5 @sm (River) - Scrum Master
+
+```
+TASKS (3):
+  Workflow: create-next-story, execute-checklist, correct-course
+
+SCRIPTS (3):
+  greeting-builder, agent-config-loader, workflow-state-manager
+
+CHECKLISTS (1):
+  story-draft-checklist
+
+TEMPLATES (1):
+  story-tmpl.yaml
+
+WORKFLOWS (8):
+  Story Dev Cycle (Phase 1), All Greenfield (Phase 3),
+  All Brownfield (Dev Cycle)
+```
+
+### 3.6 @architect (Aria) - Holistic System Architect
+
+```
+TASKS (7):
+  Workflow: document-project, create-doc (+ architecture templates),
+           spec-assess-complexity, plan-create-implementation
+  On-demand: architect-analyze-impact, collaborative-edit
+
+SCRIPTS (3):
+  greeting-builder, agent-config-loader, workflow-validator
+
+CHECKLISTS (1):
+  architect-checklist
+
+TEMPLATES (4):
+  architecture-tmpl.yaml, fullstack-architecture-tmpl.yaml,
+  front-end-architecture-tmpl.yaml, brownfield-architecture-tmpl.yaml
+
+WORKFLOWS (9):
+  All Greenfield (Phase 1), All Brownfield (Planning),
+  Brownfield Discovery (Phase 1, 4), Spec Pipeline (Phases 2, 6)
+```
+
+### 3.7 @analyst (Atlas) - Business Analyst
+
+```
+TASKS (4):
+  Workflow: facilitate-brainstorming-session, create-deep-research-prompt,
+           create-doc (+ market-research/project-brief), document-project
+
+SCRIPTS (2):
+  greeting-builder, agent-config-loader
+
+CHECKLISTS (0)
+
+TEMPLATES (4):
+  brainstorming-output-tmpl.yaml, market-research-tmpl.yaml,
+  competitor-analysis-tmpl.yaml, project-brief-tmpl.yaml
+
+DATA FILES (1):
+  brainstorming-techniques.md
+
+WORKFLOWS (5):
+  All Greenfield (Phase 1), Brownfield Fullstack (Step 1),
+  Brownfield Discovery (Phase 9), Spec Pipeline (Phase 3)
+```
+
+### 3.8 @devops (Gage) - DevOps Specialist
+
+```
+TASKS (11):
+  Workflow: environment-bootstrap, create-worktree, list-worktrees,
+           remove-worktree, merge-worktree
+  On-demand: github-devops-pre-push-quality-gate,
+             github-devops-version-management,
+             github-devops-repository-cleanup, ci-cd-configuration,
+             release-management, security-audit, search-mcp, add-mcp,
+             setup-mcp-docker, setup-github
+
+SCRIPTS (3):
+  greeting-builder, generate-greeting, agent-config-loader
+
+CHECKLISTS (2):
+  release-checklist, pre-push-checklist
+
+TEMPLATES (4):
+  github-actions-ci.yml, github-actions-cd.yml,
+  github-pr-template.md, changelog-template.md
+
+WORKFLOWS (3):
+  All Greenfield (Phase 0), Auto-Worktree
+```
+
+### 3.9 @data-engineer (Dara) - Database Architect
+
+```
+TASKS (16):
+  Workflow: db-schema-audit, security-audit
+  On-demand: setup-database, db-bootstrap, db-domain-modeling,
+             db-apply-migration, db-dry-run, db-seed, db-snapshot,
+             db-rollback, db-smoke-test, db-env-check, db-run-sql,
+             db-load-csv, db-policy-apply, db-verify-order,
+             analyze-performance, test-as-user
+
+SCRIPTS (3):
+  greeting-builder, generate-greeting, agent-config-loader
+
+CHECKLISTS (3):
+  database-design-checklist, dba-predeploy-checklist,
+  dba-rollback-checklist
+
+TEMPLATES (7):
+  schema-design-tmpl.yaml, migration-plan-tmpl.yaml,
+  index-strategy-tmpl.yaml, rls-policies-tmpl.yaml,
+  + 3 SQL templates (migration, rollback, smoke-test)
+
+DATA FILES (5):
+  database-best-practices.md, supabase-patterns.md,
+  postgres-tuning-guide.md, rls-security-patterns.md,
+  migration-safety-guide.md
+
+WORKFLOWS (1):
+  Brownfield Discovery (Phases 2, 5)
+```
+
+### 3.10 @ux-design-expert (Uma) - UX/UI Designer
+
+```
+TASKS (8+):
+  Workflow: create-doc (+ front-end-spec), generate-ai-frontend-prompt,
+           build-component, generate-documentation,
+           accessibility-wcag-checklist, calculate-roi
+  On-demand: audit-codebase, consolidate-patterns, extract-tokens,
+             setup-design-system, wireframe, tokenize, migrate
+
+SCRIPTS (3):
+  greeting-builder, generate-greeting, agent-config-loader
+
+CHECKLISTS (4):
+  pattern-audit-checklist, component-quality-checklist,
+  accessibility-wcag-checklist, migration-readiness-checklist
+
+TEMPLATES (8):
+  front-end-spec-tmpl.yaml, front-end-architecture-tmpl.yaml,
+  component-react-tmpl.tsx, shock-report-tmpl.html,
+  token-exports-css-tmpl.css, token-exports-tailwind-tmpl.js,
+  tokens-schema-tmpl.yaml, state-persistence-tmpl.yaml
+
+DATA FILES (6):
+  atomic-design-principles.md, consolidation-algorithms.md,
+  design-token-best-practices.md, roi-calculation-guide.md,
+  integration-patterns.md, wcag-compliance-guide.md
+
+WORKFLOWS (4):
+  Design System Build Quality (all 4 phases),
+  Greenfield UI/Fullstack (Phase 1),
+  Brownfield UI (Step 3), Brownfield Discovery (Phases 3, 6)
+```
+
+### 3.11 @aiox-master (Orion) - Meta Orchestrator
+
+```
+TASKS (8):
+  create-doc, shard-doc, execute-checklist, document-project,
+  correct-course, create-deep-research-prompt, modify-agent,
+  create-task, create-workflow, run-workflow-engine
+
+SCRIPTS (2):
+  greeting-builder, agent-config-loader
+
+CHECKLISTS (5):
+  architect-checklist, change-checklist, po-master-checklist,
+  story-dod-checklist, story-draft-checklist
+
+TEMPLATES (14):
+  Most YAML document templates, agent-template.yaml,
+  task-template.md, workflow-template.yaml, personalized-agent-template.md
+
+DATA FILES (4):
+  aiox-kb.md, agent-config-requirements.yaml,
+  elicitation-methods.md, technical-preferences.md
+
+WORKFLOWS: Meta-agent (creates/orchestrates workflows, not a participant)
+```
+
+### 3.12 @squad-creator (Craft) - Squad Builder
+
+```
+TASKS (8):
+  squad-creator-create, squad-creator-design, squad-creator-validate,
+  squad-creator-list, squad-creator-analyze, squad-creator-extend,
+  squad-generate-skills, squad-generate-workflow
+
+SCRIPTS (12):
+  greeting-builder, agent-config-loader,
+  squad/index, squad-loader, squad-validator, squad-generator,
+  squad-designer, squad-migrator, squad-downloader, squad-publisher,
+  squad-analyzer, squad-extender
+
+CHECKLISTS (0)
+
+TEMPLATES (19):
+  8 squad component templates (squad/ directory),
+  10 squad-template scaffold files,
+  1 workflow-template.yaml
+
+WORKFLOWS (0): Standalone expansion system, no workflow integration
+```
+
+---
+
+## 4. Phase Summaries
+
+### Phase 1: Workflows, Tasks & Agent Commands
+
+- **12 workflows** mapped with agent participation matrix
+- **61 tasks** cross-referenced to agents and workflows (36 workflow-integrated, 25 on-demand)
+- **~180 agent commands** registered
+- **9 CRITICAL broken references** in @qa agent definition
+- **3 duplicate task pairs** identified
+- **5 naming inconsistencies** documented
+
+**Detail file:** [`WORKFLOW-TASK-AGENT-ANALYSIS.md`](WORKFLOW-TASK-AGENT-ANALYSIS.md)
+
+### Phase 2: Templates, Checklists & Data Files
+
+- **161 files** analyzed across 17 categories
+- **127 connected**, **7 confirmed orphans** (all SQL), **27 weak references**
+- **Most-connected:** `po-master-checklist.md` (12+ task refs, 6 workflow refs)
+- Template engine architecture documented (loader -> validator -> elicitation -> renderer)
+
+**Detail file:** [`xref-phase2-templates.md`](xref-phase2-templates.md)
+
+### Phase 3: Development Scripts & Greeting System
+
+- **37 scripts** (.js files) analyzed across 9 functional categories
+- **0 truly orphaned** scripts (all have at least install-manifest reference)
+- **5 effectively dead** migration scripts
+- **Greeting system** fully documented: 8 files, 3 greeting levels, 2 invocation patterns
+- **Squad sub-module:** 10 scripts serving @squad-creator exclusively
+
+**Detail file:** [`xref-phase3-scripts.md`](xref-phase3-scripts.md)
+
+### Phase 4: Infrastructure Scripts & Services
+
+- **115 files** across 6 subdirectories (scripts, integrations, tools, templates, tests, root)
+- **90 JS scripts** (47 exported via index.js, 28 standalone, 15+ sub-module)
+- **5 PM adapter** integrations (ClickUp, GitHub, Jira, Local + factory)
+- **15 tool definitions** (4 CLI, 1 local, 9 MCP)
+- **5 confirmed orphans**, **4 likely orphans**, **90% actively used**
+- Clean `infrastructure <- core <- development <- product` layering confirmed
+
+**Detail file:** [`xref-phase4-infra.md`](xref-phase4-infra.md)
+
+### Phase 5: Core Modules
+
+- **130 files** across **14 subsystems**
+- **Largest:** health-check (35 files), orchestration (19 files), execution (10 files)
+- **7 orphaned/partial-orphan** modules identified
+- **3 phantom dependencies** (memory-query, session-memory, security-checker path)
+- **1 deprecated file:** config-loader.js (target removal v4.0.0)
+- All cross-subsystem dependencies documented with coupling matrix
+
+**Detail file:** [`xref-phase5-core.md`](xref-phase5-core.md)
+
+### Phase 6: Supporting Systems
+
+- **12 systems** analyzed, **111 files** cataloged
+- **3 missing/empty directories:** agent-teams/, tools/ (empty), processes/
+- **3 elicitation file duplicates** between `core/elicitation/` and `elicitation/`
+- **5 deprecated standards** docs (old Livro de Ouro versions)
+- Config system in transition: monolithic `core-config.yaml` to 4-level hierarchy
+- Full interconnection map with data flow diagram
+
+**Detail file:** [`xref-phase6-supporting.md`](xref-phase6-supporting.md)
+
+---
+
+## 5. Complete Orphan Analysis
+
+### 5.1 Confirmed Orphans (19 files)
+
+Files with **no active consumers** anywhere in the runtime codebase.
+
+#### SQL Templates (7 files) -- Phase 2
+
+| File | Location |
+|------|----------|
+| `tmpl-rls-roles.sql` | `product/templates/` |
+| `tmpl-rls-simple.sql` | `product/templates/` |
+| `tmpl-rls-tenant.sql` | `product/templates/` |
+| `tmpl-stored-proc.sql` | `product/templates/` |
+| `tmpl-trigger.sql` | `product/templates/` |
+| `tmpl-view-materialized.sql` | `product/templates/` |
+| `tmpl-view.sql` | `product/templates/` |
+
+**Recommendation:** Wire to data-engineer tasks or document as manual-use reference templates.
+
+#### Infrastructure Scripts (5 files) -- Phase 4
+
+| File | Location |
+|------|----------|
+| `changelog-generator.js` | `infrastructure/scripts/` |
+| `dashboard-status-writer.js` | `infrastructure/scripts/` |
+| `cicd-discovery.js` | `infrastructure/scripts/` |
+| `pr-review-ai.js` | `infrastructure/scripts/` |
+| `test-discovery.js` | `infrastructure/scripts/` |
+
+**Recommendation:** Archive or integrate into @devops/@qa agent workflows.
+
+#### Core Modules (2 files) -- Phase 5
+
+| File | Location |
+|------|----------|
+| `ideation-engine.js` | `core/ideation/` |
+| `timeline-manager.js` | `core/memory/` |
+
+**Recommendation:** Wire to CLI commands or agent workflows, or remove.
+
+#### Deprecated Standards (5 files) -- Phase 6
+
+| File | Location |
+|------|----------|
+| `AIOX-LIVRO-DE-OURO.md` | `docs/standards/` |
+| `AIOX-LIVRO-DE-OURO-V2.1.md` | `docs/standards/` |
+| `AIOX-LIVRO-DE-OURO-V2.1-SUMMARY.md` | `docs/standards/` |
+| `AIOX-FRAMEWORK-MASTER.md` | `docs/standards/` |
+| `V3-ARCHITECTURAL-DECISIONS.md` | `docs/standards/` |
+
+**Recommendation:** Move to `docs/standards/archive/`.
+
+### 5.2 Likely Orphans (4 files) -- Phase 4
+
+Infrastructure scripts exported via `index.js` but with minimal external consumers.
+
+| File | Reason |
+|------|--------|
+| `spot-check-validator.js` | Only index.js + install-manifest references |
+| `test-utilities-fast.js` | Only index.js + install-manifest + path-analysis |
+| `performance-and-error-resolver.js` | Only index.js + install-manifest references |
+| `atomic-layer-classifier.js` | Only index.js + install-manifest references |
+
+### 5.3 Partial Orphans (5 files) -- Phase 5
+
+Core modules that are tested or documented but not consumed by other modules.
+
+| File | Status |
+|------|--------|
+| `permissions/index.js` (+ children) | Documented but not wired to CLI/agents |
+| `utils/security-utils.js` | Has tests but unused by other core modules |
+| `core/index.esm.js` | ESM barrel prepared for future migration |
+| `registry/build-registry.js` | Standalone CLI script |
+| `registry/validate-registry.js` | Standalone CLI script |
+
+### 5.4 Dead Migration Scripts (5 files) -- Phase 3
+
+One-time scripts that have completed their purpose.
+
+| File | Original Purpose |
+|------|-----------------|
+| `apply-inline-greeting-all-agents.js` | Apply inline greeting (Story 6.1.2.5-T1) |
+| `batch-update-agents-session-context.js` | Add session context (Story 6.1.2.6.2) |
+| `agent-assignment-resolver.js` | Resolve `{TODO: Agent Name}` placeholders |
+| `task-identifier-resolver.js` | Resolve `{TODO: task identifier}` placeholders |
+| `verify-workflow-gaps.js` | Verify workflow gap fixes |
+
+### 5.5 Weak References (27 files) -- Phase 2
+
+Files referenced only in passive registries (install-manifest, service-registry, workers.csv). Most are dynamically loaded at runtime (HBS templates, IDE rules, personalization templates).
+
+### 5.6 Duplication Issues (6 files)
+
+| Files | Issue |
+|-------|-------|
+| `core/elicitation/agent-elicitation.js` vs `elicitation/agent-elicitation.js` | Identical content in two locations |
+| `core/elicitation/task-elicitation.js` vs `elicitation/task-elicitation.js` | Identical content in two locations |
+| `core/elicitation/workflow-elicitation.js` vs `elicitation/workflow-elicitation.js` | Identical content in two locations |
+
+**Recommendation:** Consolidate to `core/elicitation/` and update config references.
+
+### 5.7 Ghost Directories (3)
+
+| Directory | Status | Referenced By |
+|-----------|--------|---------------|
+| `.aiox-core/agent-teams/` | Does not exist | install-manifest, source-tree docs, core-architecture |
+| `.aiox-core/tools/` | Exists but empty | core-config.yaml, framework-config.yaml |
+| `.aiox-core/processes/` | Does not exist | Not referenced |
+
+---
+
+## 6. Complete Broken Reference Report
+
+### 6.1 CRITICAL: @qa Agent -- 9 Broken Task References
+
+The `@qa` agent definition (`agents/qa.md`) references 9 task files using non-prefixed names that do NOT exist on the filesystem.
+
+| Agent Reference | Actual File on Disk | Status |
+|----------------|---------------------|--------|
+| `generate-tests.md` | `qa-generate-tests.md` | BROKEN |
+| `manage-story-backlog.md` | `qa-backlog-add-followup.md` | BROKEN |
+| `nfr-assess.md` | `qa-nfr-assess.md` | BROKEN |
+| `review-proposal.md` | `qa-review-proposal.md` | BROKEN |
+| `review-story.md` | `qa-review-story.md` | BROKEN |
+| `risk-profile.md` | `qa-risk-profile.md` | BROKEN |
+| `run-tests.md` | `qa-run-tests.md` | BROKEN |
+| `test-design.md` | `qa-test-design.md` | BROKEN |
+| `trace-requirements.md` | `qa-trace-requirements.md` | BROKEN |
+
+**Impact:** If dependency resolution does NOT apply automatic prefix fallback, @qa commands will fail to find task files.
+
+**Fix:** Update `agents/qa.md` to use the full prefixed names matching actual files.
+
+### 6.2 Duplicate Task Files (3 pairs)
+
+| Generic | Agent-Prefixed | Used in Agent Def | Used in YAML Workflow | Issue |
+|---------|----------------|--------------------|-----------------------|-------|
+| `create-next-story.md` | `sm-create-next-story.md` | @sm uses generic | YAML uses generic | Keep generic, deprecate `sm-` |
+| `apply-qa-fixes.md` | `dev-apply-qa-fixes.md` | @dev uses generic | YAML uses `dev-` prefix | **Mismatch!** Standardize. |
+| `validate-next-story.md` | `dev-validate-next-story.md` | @po/@dev uses generic | indirect | Different tasks, both valid |
+
+### 6.3 Naming Inconsistencies (5)
+
+| Issue | Severity |
+|-------|----------|
+| `sm-create-next-story.md` vs `create-next-story.md` in docs vs YAML | MEDIUM |
+| `dev-develop-story.md` sometimes referenced without `dev-` prefix | LOW |
+| `qa-review-story.md` vs `review-story.md` in brownfield docs | MEDIUM |
+| `dev-apply-qa-fixes.md` vs `apply-qa-fixes.md` in YAML vs agent def | MEDIUM |
+| `story-dod-checklist.md` path -- checklists dir reference | MEDIUM |
+
+### 6.4 Phantom Dependencies (3 missing modules)
+
+| Referenced Path | Referenced From | Status |
+|----------------|-----------------|--------|
+| `../memory/memory-query` | execution/context-injector.js, execution/subagent-dispatcher.js | Does not exist (try/catch guarded) |
+| `../memory/session-memory` | execution/context-injector.js | Does not exist (try/catch guarded) |
+| `../../infrastructure/scripts/security-checker` | elicitation/elicitation-engine.js | Exists outside core/ at infrastructure/scripts/ |
+
+### 6.5 Planned/Future Tasks (3)
+
+| Task | Status |
+|------|--------|
+| `story-review` | "Em desenvolvimento" |
+| `epic-retrospective` | "Em desenvolvimento" |
+| `brownfield-migration` | Not yet created |
+
+---
+
+## 7. Architectural Observations
+
+### 7.1 Module Layering
+
+The framework follows a clean dependency hierarchy:
+
+```
+infrastructure/   <--   core/   <--   development/   <--   product/
+(base layer)          (imports)       (imports)            (imports)
+```
+
+- **infrastructure/** has ZERO dependencies on other AIOX modules
+- **core/** imports from infrastructure (recovery-handler, build-state-manager, executors)
+- **development/** imports from infrastructure (story-manager, greeting-builder)
+- **product/** imports from infrastructure (templates, activation-instructions)
+
+### 7.2 Configuration System Transition
+
+The config system is migrating from monolithic to layered:
+
+| Level | File | Mutability | Status |
+|-------|------|------------|--------|
+| L1 | `framework-config.yaml` | Read-only (framework) | NEW |
+| L2 | `project-config.yaml` | Editable (maintainers) | NEW |
+| L3 | *(app-specific)* | -- | Not implemented |
+| L4 | `local-config.yaml` | Editable (personal) | NEW (template only) |
+| Legacy | `core-config.yaml` | All-in-one | Still primary |
+
+### 7.3 Greeting System Architecture
+
+All 12 agents share a unified greeting system:
+- **GreetingBuilder** class with contextual, session-aware greetings
+- 3 greeting levels (minimal/named/archetypal)
+- 2 invocation patterns (direct class / CLI wrapper)
+- User preference stored in `core-config.yaml`
+
+### 7.4 Task-First Architecture
+
+Tasks are the atomic unit of work. The framework uses a strict pattern:
+- **191 task files** define all executable operations
+- Tasks are consumed by **agents** (via dependencies) and **workflows** (via step definitions)
+- Only **36 tasks** are embedded in workflow YAMLs; the remaining **155** are on-demand utilities
+- The `execute-checklist.md` meta-task can execute any checklist for any agent
+
+### 7.5 Health Check Subsystem
+
+The most self-contained subsystem with **35 files**:
+- 5 check domains (project, local, repository, deployment, services)
+- 3-tier healing with backup management
+- 3 reporter formats (console, markdown, JSON)
+- Extends a shared base class pattern
+
+### 7.6 Squad System
+
+The squad system is well-isolated:
+- **10 dedicated scripts** in `development/scripts/squad/`
+- **19 templates** (8 component + 10 scaffold + 1 workflow)
+- @squad-creator agent with 8 commands
+- No workflow integration (standalone by design)
+
+---
+
+## 8. Recommendations
+
+### Priority 1: Fix Broken References (CRITICAL)
+
+1. **Fix @qa agent task references** -- Update `agents/qa.md` to use full prefixed names (`qa-generate-tests.md` instead of `generate-tests.md`).
+2. **Standardize duplicate tasks** -- Resolve the `apply-qa-fixes.md` vs `dev-apply-qa-fixes.md` mismatch between agent definition and workflow YAML.
+
+### Priority 2: Clean Up Orphans (MEDIUM)
+
+3. **Archive 5 deprecated standards** -- Move old Livro de Ouro docs to `docs/standards/archive/`.
+4. **Consolidate 3 elicitation duplicates** -- Keep files in `core/elicitation/` only, update config references.
+5. **Wire or remove 7 SQL orphan templates** -- Connect to @data-engineer tasks or document as manual reference.
+6. **Archive 5 dead migration scripts** -- Move to `development/scripts/archive/` or delete.
+
+### Priority 3: Address Missing Features (LOW)
+
+7. **Implement memory-query.js and session-memory.js** -- Or remove try/catch references in execution modules.
+8. **Wire permissions/ system** -- Connect to CLI guard middleware or agent activation.
+9. **Resolve ghost directories** -- Either create `agent-teams/` with content or remove all references.
+10. **Populate or remove `.aiox-core/tools/`** -- Currently empty despite config references.
+
+### Priority 4: Maintenance (INFO)
+
+11. **Add missing test coverage** -- 10+ core modules lack dedicated tests (see Phase 5 detail).
+12. **Complete config migration** -- Finish transition from `core-config.yaml` to L1-L4 hierarchy.
+13. **Wire 5 orphaned infra scripts** -- Integrate `changelog-generator`, `cicd-discovery`, `test-discovery`, `pr-review-ai`, `dashboard-status-writer` into agent workflows or archive.
+
+---
+
+## 9. Phase Detail Files
+
+For complete per-file analysis, see the individual phase documents:
+
+| Phase | File | Scope |
+|-------|------|-------|
+| 1 | [`WORKFLOW-TASK-AGENT-ANALYSIS.md`](WORKFLOW-TASK-AGENT-ANALYSIS.md) | 12 workflows, 191 tasks, 11 agents |
+| 2 | [`xref-phase2-templates.md`](xref-phase2-templates.md) | 161 templates, checklists, data files |
+| 3 | [`xref-phase3-scripts.md`](xref-phase3-scripts.md) | 37 dev scripts + greeting system |
+| 4 | [`xref-phase4-infra.md`](xref-phase4-infra.md) | 115 infrastructure files |
+| 5 | [`xref-phase5-core.md`](xref-phase5-core.md) | 130 core module files |
+| 6 | [`xref-phase6-supporting.md`](xref-phase6-supporting.md) | 12 supporting systems, 111 files |
+
+---
+
+*AIOX Complete Cross-Reference Analysis*
+*Story: AIOX-XREF-001*
+*Generated: 2026-02-05*
+*Total artifacts analyzed: ~745 files across 25 entity types*