feat: implement KM-RAG methodology artifacts and core architectural standards with supporting query and service updates

.agent/skills/nexus-architecture-standards/SKILL.md

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+---
+name: nexus-architecture-standards
+description: Guidelines and automated checks for maintaining Clean Architecture and SaaS standards in the NexusReader project.
+tags: [Architecture, CleanArchitecture, .NET, MediatR, SaaS, MultiTenancy]
+version: 1.0.0
+---
+
+# NexusReader Architecture Standards
+
+This skill defines the architectural guardrails for the NexusReader project to ensure consistency, scalability, and security.
+
+## Core Rules
+
+### 1. Clean Architecture Layers
+- **Domain**: Pure business logic, entities, and enums. Zero dependencies on other layers.
+- **Application**: Use cases, MediatR handlers, and interfaces. Depends ONLY on Domain.
+- **Infrastructure**: Implementation details (DB context, AI services, Auth). Depends on Application and Domain.
+- **Web/Mobile**: Presentation layer. Depends on Application (and Infrastructure for DI setup).
+
+> [!CAUTION]
+> **Application MUST NOT depend on Infrastructure.** This is a common failure mode. Always use abstractions (interfaces) in Application and implement them in Infrastructure.
+
+### 2. Multi-Tenancy (Tenant Isolation)
+- Every entity related to user data MUST have a `TenantId` property.
+- Every query MUST filter by `TenantId` to prevent data leakage.
+- Default `TenantId` is "global" for shared resources.
+
+### 3. Error Handling
+- Use `FluentResults` (`Result<T>`) for all Application services and handlers.
+- Avoid throwing exceptions for expected business failures; use `Result.Fail()`.
+
+### 4. MediatR Patterns
+- **Queries**: Read-only operations. Should return `Result<T>`. Use `AsNoTracking()` in EF Core.
+- **Commands**: State-changing operations. Should return `Result` or `Result<T>`.
+
+## Audit Scripts
+- [ArchCheck.sh](scripts/arch_check.sh): A shell script to scan for illegal cross-layer imports.
+
+## Reference Materials
+- [Layer Dependency Matrix](artifacts/layer_matrix.md)

.agent/skills/nexus-architecture-standards/scripts/arch_check.sh

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+#!/bin/bash
+
+# Simple script to check for Clean Architecture violations in NexusReader
+
+APP_DIR="src/NexusReader.Application"
+VIOLATIONS=$(grep -r "using NexusReader.Infrastructure" "$APP_DIR")
+
+if [ -n "$VIOLATIONS" ]; then
+    echo "ERROR: Clean Architecture violations found in $APP_DIR:"
+    echo "$VIOLATIONS"
+    exit 1
+else
+    echo "SUCCESS: No illegal Infrastructure dependencies found in Application layer."
+    exit 0
+fi