Update toc.yml to restructure content sections

Reorganized sections and added new items under Concepts and How-tos.

Author: yousefi-msft

articles/microsoft-discovery/toc.yml

@@ -6,12 +6,6 @@ items:
       - name: What is Microsoft Discovery?
         href: overview-what-is-microsoft-discovery.md
         displayName: Microsoft Discovery, services, overview, introduction
-      - name: Microsoft Discovery key use cases
-        href: overview-key-scenarios.md
-        displayName: Microsoft Discovery, key scenarios, use cases, research, R&D, scientific discovery
-      - name: What is Microsoft Discovery Studio?
-        href: concept-studio.md
-        displayName: Microsoft Discovery, Studio, portal, interface, VS Code, web, UI, customization
   - name: Quickstarts
     items:
       - name: v1 to v2 transition guidance
@@ -84,31 +78,11 @@ items:
           - name: Discovery Agent types
             href: concept-discovery-agent-types.md
             displayName: Discovery Agent, agent types, prompt agent, workflow agent, orchestration
-      - name: Discovery Engine
-        items:
-          - name: Discovery Engine overview
-            href: concept-discovery-engine.md
-            displayName: Discovery Engine, cognition, tasks, autonomous research, Discovery Mode
-          - name: Cognition overview
-            href: concept-cognition-overview.md
-            displayName: cognition, reasoning loop, task management, agent selection, Discovery Mode
-          - name: Tasks and investigations
-            href: concept-tasks-investigations.md
-            displayName: tasks, investigations, workflows, task status, dependencies, validation requirements
-          - name: Files and storage assets
-            href: concept-files-storage-assets.md
-            displayName: files, storage assets, WriteResource, file types, file outputs, binary files
-          - name: Trust relationship and basic investigation patterns
-            href: concept-trust-basic-investigation-patterns.md
-            displayName: trust, validation requirements, investigation patterns, workflow patterns, task structure, autonomy
-          - name: Advanced investigation patterns
-            href: concept-advanced-investigation-patterns.md
-            displayName: investigation patterns, workflow patterns, deterministic, guided exploration, autonomous research
-      - name: Observability
+      - name: Tools
         items:
-          - name: Observability overview
-            href: concept-observability.md
-            displayName: Microsoft Discovery, observability, logs, Log Analytics, MRG, activity logs, monitoring
+          - name: Discovery Tool concepts
+            href: concept-discovery-tool.md
+            displayName: Discovery Tool, code-based tools, action-based tools
   - name: How-tos
     items:
       - name: Migration
@@ -156,60 +130,3 @@ items:
           - name: Configure customer-managed keys
             href: howto-data-encryption-at-rest.md
             displayName: Microsoft Discovery, customer-managed keys, CMK, encryption at rest, Key Vault
-      - name: Investigations & Discovery Mode
-        items:
-          - name: Build investigations with cognition
-            href: how-to-build-investigations-cognition.md
-            displayName: investigations, workflows, cognition, tasks, Discovery Mode, investigation
-          - name: Task addition and execution
-            href: how-to-task-addition-execution.md
-            displayName: tasks, dependencies, execution, results, task management
-          - name: Debug task execution
-            href: how-to-debug-task-execution.md
-            displayName: debug, troubleshoot, stuck tasks, validation, errors
-          - name: "Tutorial: Discovery Mode"
-            href: tutorial-discovery-mode.md
-            displayName: tutorial, Discovery Mode, first investigation, getting started
-      - name: Tools
-        items:
-          - name: Plan tool requirements
-            href: how-to-plan-tool-requirements.md
-            displayName: Microsoft Discovery, tool publishing, requirements, compute, dependencies, tool type
-          - name: Write action scripts
-            href: how-to-write-tool-action-scripts.md
-            displayName: Microsoft Discovery, tool publishing, action scripts, entrypoint, batch processing, output
-          - name: Create a Dockerfile
-            href: how-to-create-tool-docker-file.md
-            displayName: Microsoft Discovery, tool publishing, Dockerfile, containerize, Docker image
-          - name: Publish container image to ACR
-            href: how-to-publish-tool-to-acr.md
-            displayName: Microsoft Discovery, tool publishing, Azure Container Registry, ACR, push, tag
-          - name: Create a tool definition
-            href: how-to-create-tool-definition.md
-            displayName: Microsoft Discovery, tool definition, YAML, actions, code environment, compute, infra
-      - name: Observability
-        items:
-          - name: Access resource logs
-            href: how-to-access-resource-logs.md
-            displayName: Microsoft Discovery, logs, Managed Resource Group, MRG, Log Analytics, access
-          - name: Query workspace logs
-            href: how-to-query-workspace-logs.md
-            displayName: Microsoft Discovery, workspace, logs, Log Analytics, KQL, DiscoveryLogs_CL, correlation ID
-          - name: Query CogLoop logs
-            href: how-to-query-cognitive-loop-logs.md
-            displayName: Microsoft Discovery, CogLoop, AI orchestration, logs, Log Analytics, KQL, DiscoveryCogLoopLogs, investigation progress
-          - name: Query supercomputer logs
-            href: how-to-query-supercomputer-logs.md
-            displayName: Microsoft Discovery, supercomputer, logs, Kubernetes, KubePodInventory, KubeEvents, tool logs
-          - name: Query bookshelf knowledgebase query logs
-            href: how-to-query-bookshelf-query-logs.md
-            displayName: Microsoft Discovery, bookshelf, knowledgebase, query logs, DiscoveryLogs_CL
-          - name: Query bookshelf indexing logs
-            href: how-to-query-bookshelf-indexing-logs.md
-            displayName: Microsoft Discovery, bookshelf, indexing, logs, DiscoveryBookshelfLogs_CL
-          - name: View activity logs
-            href: how-to-view-activity-logs.md
-            displayName: Microsoft Discovery, activity logs, control plane, audit, Azure Monitor, AzureActivity
-          - name: Enable audit logging
-            href: how-to-enable-audit-logging.md
-            displayName: Microsoft Discovery, audit logging, diagnostic settings, compliance, retention, storage account, Log Analytics