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diff --git a/‎docs/commands/config-init.md‎
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@@ -92,3 +92,8 @@ htmlcov/
 *.egg-info/
 dist/
 build/
+
+# Local diagnostics and code review artifacts (never commit)
+diagnostics/
+.codereviews/
+nul
@@ -53,6 +53,19 @@ a365 config init -c path/to/config.json
 a365 config init --global
 ```
 
+**Configure custom blueprint permissions:**
+```bash
+# Add custom API permissions for your agent
+a365 config permissions --resource-app-id 00000003-0000-0000-c000-000000000000 \
+  --scopes Presence.ReadWrite,Files.Read.All
+
+# View configured permissions
+a365 config permissions
+
+# Clear all custom permissions
+a365 config permissions --reset
+```
+
 **Minimum required configuration:**
 ```json
 {
@@ -122,9 +135,27 @@ a365 setup infrastructure
 a365 setup blueprint
 a365 setup permissions mcp
 a365 setup permissions bot
+a365 setup permissions custom          # Configure custom blueprint permissions (if configured)
 a365 setup permissions copilotstudio  # Configure Copilot Studio permissions
 ```
 
+**Custom Blueprint Permissions:**
+If your agent needs additional API permissions beyond the standard set (e.g., Presence, Files, Chat, or custom APIs), configure them before running setup:
+
+```bash
+# Add custom permissions to config
+a365 config permissions --resource-app-id 00000003-0000-0000-c000-000000000000 \
+  --scopes Presence.ReadWrite,Files.Read.All
+
+# Then run setup (custom permissions applied automatically)
+a365 setup all
+
+# Or apply custom permissions separately
+a365 setup permissions custom
+```
+
+See [Custom Permissions Guide](docs/commands/setup-permissions-custom.md) for detailed examples.
+
 ### Publish & Deploy
 ```bash
 a365 publish         # Publish manifest to MOS
 
@@ -154,7 +154,35 @@ a365 config init --global
 # Record: Global config created (Yes/No)
 ```
 
-**Section 2 Status**: ✅ Pass | ❌ Fail  
+#### Test 2.5: Configure Custom Blueprint Permissions
+```bash
+# Add Microsoft Graph extended permissions
+a365 config permissions \
+  --resource-app-id 00000003-0000-0000-c000-000000000000 \
+  --scopes Presence.ReadWrite,Files.Read.All
+
+# Expected: NO PROMPTS - permission added directly to a365.config.json
+# Resource name will be auto-resolved during 'a365 setup permissions custom'
+# Verify customBlueprintPermissions array exists in config file
+# Record: Custom permission added (Yes/No)
+
+# View configured permissions
+a365 config permissions
+
+# Expected: Lists all configured custom permissions (may show appId only until setup runs)
+# Record: Permissions displayed correctly (Yes/No)
+
+# Add second custom resource
+a365 config permissions \
+  --resource-app-id 12345678-1234-1234-1234-123456789012 \
+  --scopes CustomScope.Read,CustomScope.Write
+
+# Expected: NO PROMPTS - second permission added directly
+# Resource names will be auto-resolved during setup
+# Record: Second permission added (Yes/No)
+```
+
+**Section 2 Status**: ✅ Pass | ❌ Fail
 **Notes**:
 
 ---
@@ -284,7 +312,84 @@ a365 setup permissions bot
 # Record: Bot permissions set (Yes/No)
 ```
 
-**Section 4 Status**: ✅ Pass | ❌ Fail  
+#### Test 4.5: Blueprint Permissions - Custom Resources (with Auto-Lookup)
+```bash
+# Configure custom permissions (requires Test 2.5 completed)
+a365 setup permissions custom
+
+# Expected:
+# - AUTO-LOOKUP: CLI queries Azure to resolve resource display names
+# - Output shows: "Resource name not provided, attempting auto-lookup for {appId}..."
+# - Output shows: "Auto-resolved resource name: Microsoft Graph" (or similar)
+# - OAuth2 grants created for each custom resource
+# - Inheritable permissions configured
+# - Permissions visible in Azure Portal under API permissions
+# - Success messages for each configured resource
+# - Note: ResourceName is resolved in-memory for logging only; it is NOT persisted to any config file
+
+# IMPORTANT: Verify auto-lookup messages appear in output
+# If resource not found in Azure, should show fallback: "Custom-{first 8 chars}"
+
+# Record: Custom permissions configured (Yes/No)
+# Record: Number of custom resources configured
+# Record: Auto-lookup succeeded (Yes/No)
+```
+
+#### Test 4.6: Verify Custom Permissions in Azure Portal
+```bash
+# Query blueprint application to verify custom permissions
+az ad app show --id <blueprint-app-id> --query "requiredResourceAccess[].{ResourceAppId:resourceAppId, Scopes:resourceAccess[].id}"
+
+# Expected: Shows custom resource permissions configured
+# - Microsoft Graph (00000003-0000-0000-c000-000000000000) with extended scopes
+# - Custom API resource (if configured)
+
+# Alternatively, verify in Azure Portal:
+# Navigate to: Entra ID → Applications → [Blueprint App] → API permissions
+# Verify custom permissions are listed with "Granted" status
+
+# Record: Custom permissions visible in portal (Yes/No)
+```
+
+#### Test 4.7: Verify Inheritable Permissions via Graph API
+```powershell
+# Get blueprint object ID from config
+$blueprintObjectId = (Get-Content a365.generated.config.json | ConvertFrom-Json).agentBlueprintObjectId
+
+# Get access token
+$token = az account get-access-token --resource https://graph.microsoft.com --query accessToken -o tsv
+
+# Query inheritable permissions (this is what the CLI verifies internally)
+$headers = @{ Authorization = "Bearer $token" }
+$uri = "https://graph.microsoft.com/beta/applications/microsoft.graph.agentIdentityBlueprint/$blueprintObjectId/inheritablePermissions"
+$response = Invoke-RestMethod -Uri $uri -Headers $headers
+$response | ConvertTo-Json -Depth 10
+
+# Expected response format:
+# {
+#   "value": [
+#     {
+#       "resourceAppId": "00000003-0000-0000-c000-000000000000",
+#       "resourceName": "Microsoft Graph",
+#       "scopes": ["Presence.ReadWrite", "Files.Read.All"]
+#     }
+#   ]
+# }
+
+# Verify:
+# - Each custom resource appears in the "value" array
+# - resourceAppId matches configured permissions
+# - resourceName is populated (auto-resolved during setup)
+# - All requested scopes are present
+
+# Note: This is the SAME endpoint the CLI uses to verify permissions were set correctly
+# If this query succeeds, inheritable permissions are working properly
+
+# Record: Inheritable permissions verified via Graph API (Yes/No)
+# Record: Number of resources found in response
+```
+
+**Section 4 Status**: ✅ Pass | ❌ Fail
 **Notes**:
 
 ---
@@ -306,10 +411,18 @@ a365 setup all
 # Expected:
 # - Infrastructure created
 # - Blueprint created
-# - Permissions configured
+# - MCP permissions configured
+# - Bot API permissions configured
+# - Custom blueprint permissions configured (if present in config)
+# - Messaging endpoint registered
 # - All steps completed successfully
 
+# Verify custom permissions were configured (if Test 2.5 was completed):
+# - Check output for "Configuring custom blueprint permissions..."
+# - Verify each custom resource shows "configured successfully"
+
 # Record: Setup all completed (Yes/No)
+# Record: Custom permissions included (Yes/No/N/A)
 # Record: Time taken (approximate)
 ```
 
 
@@ -190,7 +190,31 @@ Azure location [westus]:
 
 **Smart Defaults**: Uses location from existing config or Azure account
 
-### Step 9: Configuration Summary
+### Step 9: Custom Blueprint Permissions (Optional)
+
+Optionally configure custom resource permissions for your agent:
+
+```
+=== Optional: Custom Blueprint Permissions ===
+If your agent needs access to additional external resources
+(e.g. Teams presence, OneDrive files, custom APIs) beyond
+standard permissions, you can configure them here.
+Most agents do not require this.
+
+Configure custom blueprint permissions? (y/N): y
+
+Resource App ID (GUID) - press Enter when done: 00000003-0000-0000-c000-000000000000
+Scopes (comma-separated, e.g. Presence.ReadWrite,Files.Read.All): Presence.ReadWrite,Files.Read.All
+Permission added.
+
+Resource App ID (GUID) - press Enter when done:
+```
+
+Press **Enter** with no input to finish and proceed.
+
+> **Tip**: You can also add or update permissions after initial setup using `a365 config permissions`.
+
+### Step 10: Configuration Summary
 
 Review all settings before saving:
 
@@ -212,11 +236,12 @@ App Service Plan       : a365agent-app-plan
 Location               : westus
 Subscription           : My Subscription (e09e22f2-9193-4f54-a335-01f59575eefd)
 Tenant                 : adfa4542-3e1e-46f5-9c70-3df0b15b3f6c
+Custom Permissions     : 1 configured
 
 Do you want to customize any derived names? (y/N):
 ```
 
-### Step 10: Name Customization (Optional)
+### Step 11: Name Customization (Optional)
 
 Optionally customize generated names:
 
@@ -230,7 +255,7 @@ Agent User Principal Name [agent.myagent.11140916@yourdomain.onmicrosoft.com]:
 Agent User Display Name [myagent Agent User]:
 ```
 
-### Step 11: Confirmation
+### Step 12: Confirmation
 
 Final confirmation to save: