diff --git a/.github/workflows/go-logger.lock.yml b/.github/workflows/go-logger.lock.yml
index 86cb698ffbe..af22ed6fcba 100644
--- a/.github/workflows/go-logger.lock.yml
+++ b/.github/workflows/go-logger.lock.yml
@@ -90,7 +90,7 @@ jobs:
         with:
           persist-credentials: false
       - name: Set up Node.js
-        uses: actions/setup-node@a0853c24544627f65ddf259abe73b1d18a591444
+        uses: actions/setup-node@2028fbc5c25fe9cf00d9f06a71cc4710d4507903
         with:
           cache: npm
           cache-dependency-path: pkg/workflow/js/package-lock.json
diff --git a/.github/workflows/technical-doc-writer.lock.yml b/.github/workflows/technical-doc-writer.lock.yml
index 24a193cc30f..0e2f89b7799 100644
--- a/.github/workflows/technical-doc-writer.lock.yml
+++ b/.github/workflows/technical-doc-writer.lock.yml
@@ -493,7 +493,7 @@ jobs:
         with:
           persist-credentials: false
       - name: Setup Node.js
-        uses: actions/setup-node@a0853c24544627f65ddf259abe73b1d18a591444
+        uses: actions/setup-node@2028fbc5c25fe9cf00d9f06a71cc4710d4507903
         with:
           cache: npm
           cache-dependency-path: docs/package-lock.json
diff --git a/.github/workflows/tidy.lock.yml b/.github/workflows/tidy.lock.yml
index 964804b1d3f..1db02fce2cb 100644
--- a/.github/workflows/tidy.lock.yml
+++ b/.github/workflows/tidy.lock.yml
@@ -454,7 +454,7 @@ jobs:
         with:
           persist-credentials: false
       - name: Set up Node.js
-        uses: actions/setup-node@a0853c24544627f65ddf259abe73b1d18a591444
+        uses: actions/setup-node@2028fbc5c25fe9cf00d9f06a71cc4710d4507903
         with:
           cache: npm
           cache-dependency-path: pkg/workflow/js/package-lock.json
diff --git a/pkg/cli/commands_compile_workflow_test.go b/pkg/cli/commands_compile_workflow_test.go
index b3761c20230..2641507f992 100644
--- a/pkg/cli/commands_compile_workflow_test.go
+++ b/pkg/cli/commands_compile_workflow_test.go
@@ -28,6 +28,8 @@ on:
     branches: [main]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 ---
 
 # Test Workflow
@@ -58,6 +60,8 @@ on:
     - cron: "0 9 * * 1"
 permissions:
   contents: write
+  issues: read
+  pull-requests: read
 ---
 
 # Verbose Test Workflow
@@ -88,6 +92,8 @@ on:
     branches: [main]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 ---
 
 # Engine Override Test
@@ -421,6 +427,8 @@ on:
     branches: [main]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 ---
 
 # Test Workflow
@@ -460,6 +468,8 @@ on:
     branches: [main]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 ---
 
 # Test Workflow
diff --git a/pkg/cli/commands_test.go b/pkg/cli/commands_test.go
index 168d060babf..ec23f53e947 100644
--- a/pkg/cli/commands_test.go
+++ b/pkg/cli/commands_test.go
@@ -143,6 +143,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 ---
 
 # Test Workflow for No Emit
diff --git a/pkg/cli/compile_dependabot_test.go b/pkg/cli/compile_dependabot_test.go
index ed32e3c72e8..015216b2093 100644
--- a/pkg/cli/compile_dependabot_test.go
+++ b/pkg/cli/compile_dependabot_test.go
@@ -37,6 +37,8 @@ func TestCompileDependabotIntegration(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 steps:
   - run: npx @playwright/mcp@latest --help
 ---
@@ -159,6 +161,8 @@ func TestCompileDependabotNoDependencies(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 ---
 
 # Test Workflow
@@ -239,6 +243,8 @@ func TestCompileDependabotPreserveExisting(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 steps:
   - run: npx @playwright/mcp@latest --help
 ---
@@ -348,6 +354,8 @@ func TestCompileDependabotMergeExistingNpm(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 steps:
   - run: npx @playwright/mcp@latest --help
 ---
diff --git a/pkg/cli/compile_instructions_test.go b/pkg/cli/compile_instructions_test.go
index 7afa7649336..e313afb121c 100644
--- a/pkg/cli/compile_instructions_test.go
+++ b/pkg/cli/compile_instructions_test.go
@@ -51,6 +51,8 @@ func TestCompileDoesNotWriteInstructions(t *testing.T) {
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
@@ -153,6 +155,8 @@ func TestCompileDoesNotWriteInstructionsWhenCompilingAll(t *testing.T) {
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
diff --git a/pkg/workflow/action_sha_validation_test.go b/pkg/workflow/action_sha_validation_test.go
index 094537217ae..be04a10af80 100644
--- a/pkg/workflow/action_sha_validation_test.go
+++ b/pkg/workflow/action_sha_validation_test.go
@@ -19,7 +19,8 @@ on: push
 engine: copilot
 permissions:
   contents: read
----
+  issues: read
+  pull-requests: read
 
 # Test Workflow
 This is a test workflow to verify SHA pinning.
@@ -84,6 +85,7 @@ engine: copilot
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 safe-outputs:
   create-issue:
 ---
@@ -143,7 +145,8 @@ on: push
 engine: copilot
 permissions:
   contents: read
----
+  issues: read
+  pull-requests: read
 
 # Simple Test
 Just a simple test workflow.
diff --git a/pkg/workflow/agentic_output_test.go b/pkg/workflow/agentic_output_test.go
index 70a39db3c40..8ecaf0b5e46 100644
--- a/pkg/workflow/agentic_output_test.go
+++ b/pkg/workflow/agentic_output_test.go
@@ -24,6 +24,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues]
@@ -123,6 +124,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues]
@@ -245,6 +247,8 @@ func TestEngineOutputCleanupExcludesTmpFiles(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues]
diff --git a/pkg/workflow/allowed_domains_sanitization_test.go b/pkg/workflow/allowed_domains_sanitization_test.go
index dbc43add196..1c84b2bb79c 100644
--- a/pkg/workflow/allowed_domains_sanitization_test.go
+++ b/pkg/workflow/allowed_domains_sanitization_test.go
@@ -22,6 +22,8 @@ func TestAllowedDomainsFromNetworkConfig(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 network:
   allowed:
@@ -52,6 +54,8 @@ Test workflow with network permissions.
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 network:
   allowed:
@@ -78,6 +82,8 @@ Test workflow with network permissions.
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 network: defaults
 safe-outputs:
@@ -104,6 +110,8 @@ Test workflow with defaults network.
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 safe-outputs:
   create-issue:
@@ -128,6 +136,8 @@ Test workflow without network config.
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 network:
   allowed:
@@ -234,6 +244,8 @@ func TestManualAllowedDomainsHasPriority(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 network:
   allowed:
@@ -263,6 +275,8 @@ Test that manual allowed-domains takes precedence.
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 network:
   allowed:
diff --git a/pkg/workflow/aw_info_steps_test.go b/pkg/workflow/aw_info_steps_test.go
index 5f44d04de10..e934d87b6db 100644
--- a/pkg/workflow/aw_info_steps_test.go
+++ b/pkg/workflow/aw_info_steps_test.go
@@ -20,6 +20,8 @@ func TestAwInfoStepsFirewall(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 network:
   firewall: true
@@ -38,6 +40,8 @@ This workflow tests that firewall type is set to squid when enabled.
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 network:
   firewall: false
@@ -56,6 +60,8 @@ This workflow tests that firewall type is empty when disabled.
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
diff --git a/pkg/workflow/aw_info_tmp_test.go b/pkg/workflow/aw_info_tmp_test.go
index 01d066e0bdd..565cbca20c2 100644
--- a/pkg/workflow/aw_info_tmp_test.go
+++ b/pkg/workflow/aw_info_tmp_test.go
@@ -21,6 +21,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues]
diff --git a/pkg/workflow/cache_memory_import_test.go b/pkg/workflow/cache_memory_import_test.go
index 14b5183190d..b90130ce5ce 100644
--- a/pkg/workflow/cache_memory_import_test.go
+++ b/pkg/workflow/cache_memory_import_test.go
@@ -41,6 +41,8 @@ name: Test Import Only
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 imports:
   - shared/cache-config.md
diff --git a/pkg/workflow/cache_memory_integration_test.go b/pkg/workflow/cache_memory_integration_test.go
index ce6742478aa..22edf58b09c 100644
--- a/pkg/workflow/cache_memory_integration_test.go
+++ b/pkg/workflow/cache_memory_integration_test.go
@@ -21,6 +21,8 @@ name: Test Cache Memory Single
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 tools:
   cache-memory: true
@@ -52,6 +54,8 @@ name: Test Cache Memory Multiple
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 tools:
   cache-memory:
@@ -93,6 +97,8 @@ name: Test Cache Memory Multiple No Keys
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 tools:
   cache-memory:
diff --git a/pkg/workflow/checkout_optimization_test.go b/pkg/workflow/checkout_optimization_test.go
index fd3669c4d18..9fac8fb80ea 100644
--- a/pkg/workflow/checkout_optimization_test.go
+++ b/pkg/workflow/checkout_optimization_test.go
@@ -22,7 +22,7 @@ on:
     types: [opened]
 tools:
   github:
-    allowed: [list_issues]
+    toolsets: [issues]
 engine: claude
 ---`,
 			expectedHasCheckout: true,
@@ -39,7 +39,7 @@ permissions:
   pull-requests: read
 tools:
   github:
-    allowed: [list_issues]
+    toolsets: [issues, pull_requests]
 engine: claude
 ---`,
 			expectedHasCheckout: false,
@@ -54,9 +54,10 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
-    allowed: [list_issues]
+    toolsets: [repos, issues, pull_requests]
 engine: claude
 ---`,
 			expectedHasCheckout: true,
@@ -71,9 +72,10 @@ on:
 permissions:
   contents: write
   issues: write
+  pull-requests: read
 tools:
   github:
-    allowed: [list_issues]
+    toolsets: [repos, issues, pull_requests]
 engine: claude
 ---`,
 			expectedHasCheckout: true,
@@ -88,7 +90,7 @@ on:
 permissions: read-all
 tools:
   github:
-    allowed: [list_issues]
+    toolsets: [issues]
 engine: claude
 ---`,
 			expectedHasCheckout: true,
@@ -103,7 +105,7 @@ on:
 permissions: write-all
 tools:
   github:
-    allowed: [list_issues]
+    toolsets: [issues]
 engine: claude
 ---`,
 			expectedHasCheckout: true,
@@ -118,6 +120,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 steps:
   - name: Custom checkout
     uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8
@@ -127,7 +130,7 @@ steps:
     run: echo "custom setup"
 tools:
   github:
-    allowed: [list_issues]
+    toolsets: [issues]
 engine: claude
 ---`,
 			expectedHasCheckout: false,
@@ -142,6 +145,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 steps:
   - name: Setup Node
     uses: actions/setup-node@v4
@@ -151,7 +155,7 @@ steps:
     run: npm install
 tools:
   github:
-    allowed: [list_issues]
+    toolsets: [issues]
 engine: claude
 ---`,
 			expectedHasCheckout: true,
@@ -175,7 +179,7 @@ steps:
     run: npm install
 tools:
   github:
-    allowed: [list_issues]
+    toolsets: [issues, pull_requests]
 engine: claude
 ---`,
 			expectedHasCheckout: false,
diff --git a/pkg/workflow/checkout_persist_credentials_test.go b/pkg/workflow/checkout_persist_credentials_test.go
index 73bda8b7e51..b2c6a7b5b43 100644
--- a/pkg/workflow/checkout_persist_credentials_test.go
+++ b/pkg/workflow/checkout_persist_credentials_test.go
@@ -22,6 +22,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues]
@@ -38,6 +39,8 @@ on:
 permissions:
   contents: read
   actions: read
+  issues: read
+  pull-requests: read
 safe-outputs:
   create-issue:
     assignees: [user1]
@@ -54,6 +57,8 @@ on:
 permissions:
   contents: read
   actions: read
+  issues: read
+  pull-requests: read
 safe-outputs:
   create-pull-request:
 engine: claude
@@ -69,6 +74,8 @@ on:
 permissions:
   contents: read
   actions: read
+  issues: read
+  pull-requests: read
 safe-outputs:
   push-to-pull-request-branch:
 engine: claude
@@ -83,6 +90,8 @@ on:
 permissions:
   contents: read
   actions: read
+  issues: read
+  pull-requests: read
 safe-outputs:
   upload-assets:
 engine: claude
@@ -98,6 +107,8 @@ on:
 permissions:
   contents: read
   actions: read
+  issues: read
+  pull-requests: read
 safe-outputs:
   create-agent-task:
 engine: claude
diff --git a/pkg/workflow/claude_settings_tmp_test.go b/pkg/workflow/claude_settings_tmp_test.go
index cbc19dfe74a..533dac17ca5 100644
--- a/pkg/workflow/claude_settings_tmp_test.go
+++ b/pkg/workflow/claude_settings_tmp_test.go
@@ -21,6 +21,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues]
diff --git a/pkg/workflow/compile_test.go b/pkg/workflow/compile_test.go
index 9fe3cac74b8..d45710f73a7 100644
--- a/pkg/workflow/compile_test.go
+++ b/pkg/workflow/compile_test.go
@@ -21,6 +21,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 engine: claude
 safe-outputs:
   create-issue:
@@ -88,6 +89,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 engine: claude
 ---
 
@@ -214,6 +216,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues]
@@ -691,6 +694,7 @@ on: push
 permissions:
   contents: read
   pull-requests: write
+  issues: read
 engine: claude
 safe-outputs:
   create-pull-request:
@@ -758,6 +762,7 @@ on: push
 permissions:
   contents: read
   pull-requests: write
+  issues: read
 tools:
   github:
     allowed: [list_issues]
@@ -871,6 +876,7 @@ on: push
 permissions:
   contents: read
   pull-requests: write
+  issues: read
 tools:
   github:
     allowed: [list_issues]
@@ -946,6 +952,7 @@ on: push
 permissions:
   contents: read
   pull-requests: write
+  issues: read
 tools:
   github:
     allowed: [list_issues]
@@ -1196,6 +1203,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 engine: claude
 safe-outputs:
   add-labels:
@@ -1281,6 +1289,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 engine: claude
 safe-outputs:
   add-labels:
@@ -1685,6 +1694,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 engine: claude
 safe-outputs:
   add-labels:
@@ -1730,6 +1740,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 engine: claude
 safe-outputs:
   add-labels: {}
@@ -1774,6 +1785,7 @@ on: push
 permissions:
   contents: read
   pull-requests: write
+  issues: read
 engine: claude
 safe-outputs:
   create-pull-request:
@@ -1819,6 +1831,7 @@ on: push
 permissions:
   contents: read
   pull-requests: write
+  issues: read
 engine: claude
 safe-outputs:
   create-pull-request:
diff --git a/pkg/workflow/compiler_expression_size_test.go b/pkg/workflow/compiler_expression_size_test.go
index c7d929819b3..9113b38fb31 100644
--- a/pkg/workflow/compiler_expression_size_test.go
+++ b/pkg/workflow/compiler_expression_size_test.go
@@ -25,6 +25,7 @@ timeout_minutes: 10
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues, get_issue]
@@ -64,6 +65,7 @@ timeout_minutes: 10
 permissions:
   contents: read
   pull-requests: write
+  issues: read
 tools:
   github:
     allowed: [list_issues]
diff --git a/pkg/workflow/compiler_file_size_test.go b/pkg/workflow/compiler_file_size_test.go
index 6eaa2db03ea..fa970d282e5 100644
--- a/pkg/workflow/compiler_file_size_test.go
+++ b/pkg/workflow/compiler_file_size_test.go
@@ -25,6 +25,7 @@ timeout_minutes: 10
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues, create_issue]
@@ -65,6 +66,7 @@ timeout_minutes: 10
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues, create_issue]
diff --git a/pkg/workflow/compiler_template_validation_test.go b/pkg/workflow/compiler_template_validation_test.go
index e06565a254c..7f57653891b 100644
--- a/pkg/workflow/compiler_template_validation_test.go
+++ b/pkg/workflow/compiler_template_validation_test.go
@@ -23,7 +23,6 @@ func TestCompilerRejectsIncludesInTemplateRegions(t *testing.T) {
 on: issues
 permissions:
   issues: write
----
 
 # Valid Workflow
 
@@ -40,7 +39,6 @@ This is valid.
 on: issues
 permissions:
   issues: write
----
 
 # Invalid Workflow
 
@@ -57,7 +55,6 @@ This should fail.
 on: pull_request
 permissions:
   pull-requests: write
----
 
 # Invalid Workflow with Import
 
@@ -73,7 +70,6 @@ permissions:
 on: issues
 permissions:
   issues: write
----
 
 # Valid Complex Workflow
 
diff --git a/pkg/workflow/compiler_test.go b/pkg/workflow/compiler_test.go
index 801d517b7db..21c6da71d7b 100644
--- a/pkg/workflow/compiler_test.go
+++ b/pkg/workflow/compiler_test.go
@@ -25,6 +25,7 @@ timeout_minutes: 10
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues, create_issue]
@@ -173,7 +174,9 @@ on:
   issues:
     types: [opened]
 permissions:
+  contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [add_issue_comment]
@@ -195,7 +198,9 @@ on:
   issues:
     types: [opened]
 permissions:
+  contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [add_issue_comment]
@@ -1570,6 +1575,8 @@ func TestWorkflowNameWithColon(t *testing.T) {
 timeout_minutes: 10
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues]
@@ -1725,6 +1732,8 @@ timeout_minutes: 15
 permissions:
   contents: read
   models: read
+  issues: read
+  pull-requests: read
 
 mcp-servers:
   notionApi:
@@ -2538,6 +2547,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [get_issue]
@@ -2922,6 +2932,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [get_issue]
@@ -2987,6 +2998,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -3006,6 +3018,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -3024,6 +3037,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -3044,6 +3058,7 @@ if: github.actor != 'dependabot[bot]'
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -3065,6 +3080,7 @@ if: github.actor != 'dependabot[bot]'
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -3083,6 +3099,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -3171,6 +3188,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -3191,6 +3209,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -3210,6 +3229,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -3232,6 +3252,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -3352,6 +3373,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues
@@ -3373,6 +3395,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 invalid: yaml: syntax
   more: bad
 engine: claude
@@ -3411,6 +3434,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: ["list_issues]
@@ -3431,6 +3455,8 @@ Invalid YAML with unclosed quote.`,
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 permissions:
   issues: write
 engine: claude
@@ -3451,6 +3477,7 @@ on: push
 permissions:
   contents: read
   issues: yes_please
+  pull-requests: read
 engine: claude
 ---
 
@@ -3513,6 +3540,8 @@ on: push
 timeout_minutes: 05.5
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
@@ -3535,6 +3564,8 @@ tools:
   claude: [
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
@@ -3755,6 +3786,8 @@ name: Test Cache Workflow
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 cache:
   key: node-modules-${{ hashFiles('package-lock.json') }}
@@ -3786,6 +3819,8 @@ name: Test Multi Cache Workflow
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 cache:
   - key: node-modules-${{ hashFiles('package-lock.json') }}
@@ -3829,6 +3864,8 @@ name: Test Full Cache Workflow
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 cache:
   key: full-cache-${{ github.sha }}
@@ -3921,6 +3958,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues]
@@ -4014,6 +4052,7 @@ on: issues
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues]
@@ -4201,6 +4240,7 @@ on:
 permissions:
   contents: write
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues, create_issue]
@@ -4371,6 +4411,8 @@ on: push
 permissions:
   contents: read
 %s
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
@@ -4733,6 +4775,8 @@ on: push
 permissions:
   contents: read
 %s
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
@@ -4897,6 +4941,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -4922,6 +4967,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -4948,6 +4994,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -4972,6 +5019,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -4996,6 +5044,7 @@ if: github.actor != 'dependabot[bot]'
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -5018,6 +5067,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -5040,6 +5090,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -5062,6 +5113,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -5083,6 +5135,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -5171,6 +5224,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -5197,6 +5251,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -5217,6 +5272,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -5236,6 +5292,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -5446,6 +5503,8 @@ on:
     branches: [main]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 tools:
   github:
@@ -5466,6 +5525,8 @@ on:
     branches: [main]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 tools:
   github:
@@ -5482,6 +5543,8 @@ on:
     branches: [main]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 tools:
   github:
@@ -5610,6 +5673,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [get_issue]
@@ -5627,6 +5691,8 @@ on:
   stop-after: +1h
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 tools:
   github:
     allowed: [list_commits]
@@ -5645,6 +5711,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [get_issue]
@@ -5742,6 +5809,8 @@ func TestPostStepsIndentationFix(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues]
@@ -5852,6 +5921,8 @@ func TestPromptUploadArtifact(t *testing.T) {
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 ---
 
diff --git a/pkg/workflow/copilot_engine_test.go b/pkg/workflow/copilot_engine_test.go
index b53bb41646c..5a420d648a9 100644
--- a/pkg/workflow/copilot_engine_test.go
+++ b/pkg/workflow/copilot_engine_test.go
@@ -865,6 +865,8 @@ func TestCopilotEngineLogParsingUsesCorrectLogFile(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 tools:
   github:
diff --git a/pkg/workflow/create_agent_task_integration_test.go b/pkg/workflow/create_agent_task_integration_test.go
index 9dfa807aa7c..107e0116adf 100644
--- a/pkg/workflow/create_agent_task_integration_test.go
+++ b/pkg/workflow/create_agent_task_integration_test.go
@@ -18,6 +18,8 @@ func TestAgentTaskWorkflowCompilation(t *testing.T) {
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 safe-outputs:
   create-agent-task:
@@ -108,6 +110,8 @@ func TestAgentTaskWorkflowWithTargetRepo(t *testing.T) {
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 safe-outputs:
   create-agent-task:
diff --git a/pkg/workflow/create_issue_assignees_integration_test.go b/pkg/workflow/create_issue_assignees_integration_test.go
index bedeaf0a702..0711f0dead6 100644
--- a/pkg/workflow/create_issue_assignees_integration_test.go
+++ b/pkg/workflow/create_issue_assignees_integration_test.go
@@ -23,6 +23,8 @@ on:
     types: [opened]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 safe-outputs:
   create-issue:
@@ -146,6 +148,8 @@ on:
     types: [opened]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 safe-outputs:
   create-issue:
@@ -208,6 +212,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 safe-outputs:
   create-issue:
@@ -271,6 +277,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 safe-outputs:
   create-issue:
diff --git a/pkg/workflow/create_issue_backward_compat_test.go b/pkg/workflow/create_issue_backward_compat_test.go
index 6f40626a1ad..dea6f00629c 100644
--- a/pkg/workflow/create_issue_backward_compat_test.go
+++ b/pkg/workflow/create_issue_backward_compat_test.go
@@ -24,6 +24,8 @@ on:
     types: [opened]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 safe-outputs:
   create-issue:
@@ -98,6 +100,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 safe-outputs:
   create-issue:
diff --git a/pkg/workflow/create_issue_subissue_test.go b/pkg/workflow/create_issue_subissue_test.go
index 5cb3c4e7af3..02cb18a3330 100644
--- a/pkg/workflow/create_issue_subissue_test.go
+++ b/pkg/workflow/create_issue_subissue_test.go
@@ -81,6 +81,8 @@ on:
     types: [opened]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 safe-outputs:
   create-issue:
diff --git a/pkg/workflow/create_pr_review_comment_test.go b/pkg/workflow/create_pr_review_comment_test.go
index d9aac5d9681..ded6dea9758 100644
--- a/pkg/workflow/create_pr_review_comment_test.go
+++ b/pkg/workflow/create_pr_review_comment_test.go
@@ -22,6 +22,7 @@ on: pull_request
 permissions:
   contents: read
   pull-requests: write
+  issues: read
 engine: claude
 safe-outputs:
   create-pull-request-review-comment:
diff --git a/pkg/workflow/create_pull_request_reviewers_integration_test.go b/pkg/workflow/create_pull_request_reviewers_integration_test.go
index 16c0172f4fb..2a5ba67aac7 100644
--- a/pkg/workflow/create_pull_request_reviewers_integration_test.go
+++ b/pkg/workflow/create_pull_request_reviewers_integration_test.go
@@ -21,6 +21,8 @@ on: push
 permissions:
   contents: read
   actions: read
+  issues: read
+  pull-requests: read
 engine: copilot
 safe-outputs:
   create-pull-request:
@@ -118,6 +120,8 @@ on: push
 permissions:
   contents: read
   actions: read
+  issues: read
+  pull-requests: read
 engine: copilot
 safe-outputs:
   create-pull-request:
@@ -180,6 +184,8 @@ on: push
 permissions:
   contents: read
   actions: read
+  issues: read
+  pull-requests: read
 engine: copilot
 safe-outputs:
   create-pull-request:
diff --git a/pkg/workflow/custom_engine_integration_test.go b/pkg/workflow/custom_engine_integration_test.go
index 705ea83ef8c..f41f90f19ea 100644
--- a/pkg/workflow/custom_engine_integration_test.go
+++ b/pkg/workflow/custom_engine_integration_test.go
@@ -30,6 +30,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 engine:
   id: custom
   steps:
diff --git a/pkg/workflow/engine_config_test.go b/pkg/workflow/engine_config_test.go
index 221487b131d..98b41f2dd17 100644
--- a/pkg/workflow/engine_config_test.go
+++ b/pkg/workflow/engine_config_test.go
@@ -316,6 +316,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 engine: claude
 ---
 
@@ -332,6 +333,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 engine:
   id: claude
   version: beta
@@ -351,6 +353,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 engine:
   id: codex
   model: gpt-4o
diff --git a/pkg/workflow/engine_includes_test.go b/pkg/workflow/engine_includes_test.go
index f972ac0f373..5720017a0ca 100644
--- a/pkg/workflow/engine_includes_test.go
+++ b/pkg/workflow/engine_includes_test.go
@@ -408,6 +408,8 @@ on:
 permissions:
   contents: read
   models: read
+  issues: read
+  pull-requests: read
 imports:
   - shared/actions-ai-inference.md
 ---
diff --git a/pkg/workflow/fetch_integration_test.go b/pkg/workflow/fetch_integration_test.go
index cc2b4c636a2..07cf9b04e8f 100644
--- a/pkg/workflow/fetch_integration_test.go
+++ b/pkg/workflow/fetch_integration_test.go
@@ -18,6 +18,8 @@ func TestWebFetchMCPServerAddition(t *testing.T) {
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: codex
 tools:
   web-fetch:
@@ -79,6 +81,8 @@ func TestWebFetchNotAddedForClaudeEngine(t *testing.T) {
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 tools:
   web-fetch:
@@ -142,6 +146,8 @@ func TestNoWebFetchNoMCPFetchServer(t *testing.T) {
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: codex
 tools:
   bash:
diff --git a/pkg/workflow/git_config_test.go b/pkg/workflow/git_config_test.go
index fa9be09a31c..779f9dbaf6c 100644
--- a/pkg/workflow/git_config_test.go
+++ b/pkg/workflow/git_config_test.go
@@ -21,6 +21,8 @@ func TestGitConfigurationInMainJob(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 ---
 
diff --git a/pkg/workflow/imports_markdown_test.go b/pkg/workflow/imports_markdown_test.go
index 7575bf09b88..8bdcfea4d89 100644
--- a/pkg/workflow/imports_markdown_test.go
+++ b/pkg/workflow/imports_markdown_test.go
@@ -65,6 +65,8 @@ This is common setup content that should be prepended.
 on: issues
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 imports:
   - shared/common.md
@@ -84,6 +86,8 @@ This is the main workflow content.`,
 on: issues
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 imports:
   - shared/common.md
@@ -188,6 +192,8 @@ This comes from @include directive.`
 on: issues
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 imports:
   - shared/import.md
diff --git a/pkg/workflow/label_filter_test.go b/pkg/workflow/label_filter_test.go
index 5a0f413c485..93ec66d61a0 100644
--- a/pkg/workflow/label_filter_test.go
+++ b/pkg/workflow/label_filter_test.go
@@ -34,6 +34,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -53,6 +54,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -72,6 +74,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -91,6 +94,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -110,6 +114,7 @@ on:
 permissions:
   contents: read
   pull-requests: write
+  issues: read
 
 tools:
   github:
@@ -129,6 +134,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -147,6 +153,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
@@ -218,6 +225,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 
 tools:
   github:
diff --git a/pkg/workflow/manifest_test.go b/pkg/workflow/manifest_test.go
index 8a1032a7254..d28ef34ae25 100644
--- a/pkg/workflow/manifest_test.go
+++ b/pkg/workflow/manifest_test.go
@@ -58,6 +58,8 @@ Be helpful and concise.`
 on: issues
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 imports:
   - shared/tools.md
@@ -78,6 +80,8 @@ Handle the issue.`,
 on: issues
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 imports:
   - shared/tools.md
@@ -96,6 +100,8 @@ Handle the issue.`,
 on: issues
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
@@ -114,6 +120,8 @@ Handle the issue.`,
 on: issues
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
diff --git a/pkg/workflow/max_turns_test.go b/pkg/workflow/max_turns_test.go
index 8ccf567c194..a4dc56a3292 100644
--- a/pkg/workflow/max_turns_test.go
+++ b/pkg/workflow/max_turns_test.go
@@ -21,6 +21,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine:
   id: claude
   max-turns: 3
@@ -42,6 +44,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 tools:
   github:
@@ -61,6 +65,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine:
   id: claude
   max-turns: 10
@@ -176,6 +182,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine:
   id: claude
   max-turns: 5
@@ -191,6 +199,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine:
   id: claude
   max-turns: "invalid"
@@ -206,6 +216,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine:
   id: claude
   max-turns: 0
@@ -250,6 +262,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine:
   id: custom
   max-turns: 5
diff --git a/pkg/workflow/max_turns_validation_test.go b/pkg/workflow/max_turns_validation_test.go
index a1c940995b3..e75825a2c99 100644
--- a/pkg/workflow/max_turns_validation_test.go
+++ b/pkg/workflow/max_turns_validation_test.go
@@ -22,6 +22,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine:
   id: codex
   max-turns: 5
@@ -41,6 +43,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine:
   id: claude
   max-turns: 5
@@ -59,6 +63,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: codex
 ---
 
@@ -75,6 +81,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
diff --git a/pkg/workflow/mcp_config_compilation_test.go b/pkg/workflow/mcp_config_compilation_test.go
index 17f9c4c4848..e95caf71d7c 100644
--- a/pkg/workflow/mcp_config_compilation_test.go
+++ b/pkg/workflow/mcp_config_compilation_test.go
@@ -14,6 +14,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 network: defaults
 mcp-servers:
@@ -124,6 +126,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 mcp-servers:
   test-server:
diff --git a/pkg/workflow/patch_generation_test.go b/pkg/workflow/patch_generation_test.go
index ea2eb13e52d..ef336f44943 100644
--- a/pkg/workflow/patch_generation_test.go
+++ b/pkg/workflow/patch_generation_test.go
@@ -20,6 +20,8 @@ func TestPullRequestPatchGeneration(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 safe-outputs:
   create-pull-request:
diff --git a/pkg/workflow/permissions_excess_compilation_test.go b/pkg/workflow/permissions_excess_compilation_test.go
index 84ae9c572ba..ab6fd9b8c77 100644
--- a/pkg/workflow/permissions_excess_compilation_test.go
+++ b/pkg/workflow/permissions_excess_compilation_test.go
@@ -25,6 +25,7 @@ permissions:
   contents: read
   issues: read
   actions: read
+  pull-requests: read
 engine: copilot
 tools:
   github:
@@ -48,6 +49,7 @@ permissions:
   contents: write
   issues: write
   actions: read
+  pull-requests: read
 engine: copilot
 tools:
   github:
@@ -65,6 +67,8 @@ tools:
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 tools:
   github:
@@ -86,6 +90,8 @@ network:
 on: push
 permissions:
   contents: write
+  issues: read
+  pull-requests: read
 engine: copilot
 tools:
   github:
@@ -211,6 +217,7 @@ permissions:
   contents: write
   issues: write
   actions: read
+  pull-requests: read
 engine: copilot
 tools:
   github:
diff --git a/pkg/workflow/permissions_import_test.go b/pkg/workflow/permissions_import_test.go
index df633abedf0..7c332594adf 100644
--- a/pkg/workflow/permissions_import_test.go
+++ b/pkg/workflow/permissions_import_test.go
@@ -102,7 +102,6 @@ func TestPermissionsImportIntegration(t *testing.T) {
 	sharedWorkflowContent := `---
 permissions:
   actions: read
----
 
 # Shared workflow with permissions
 `
@@ -206,7 +205,8 @@ tools:
 		sharedWorkflowUpgradeContent := `---
 permissions:
   contents: write
----
+  issues: read
+  pull-requests: read
 
 # Shared workflow with write permission
 `
@@ -295,7 +295,7 @@ func TestExtractPermissionsFromContent(t *testing.T) {
 permissions:
   contents: read
   issues: write
----
+  pull-requests: read
 # Content`,
 			expected: `{"contents":"read","issues":"write"}`,
 			wantErr:  false,
diff --git a/pkg/workflow/pinned_actions_comment_test.go b/pkg/workflow/pinned_actions_comment_test.go
index 7b3c06e3732..f4743cd1047 100644
--- a/pkg/workflow/pinned_actions_comment_test.go
+++ b/pkg/workflow/pinned_actions_comment_test.go
@@ -237,6 +237,8 @@ func TestPinnedActionsCommentInGeneratedYAML(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 ---
 
diff --git a/pkg/workflow/pr_checkout_test.go b/pkg/workflow/pr_checkout_test.go
index 1805e4ac158..29b982479e1 100644
--- a/pkg/workflow/pr_checkout_test.go
+++ b/pkg/workflow/pr_checkout_test.go
@@ -25,6 +25,8 @@ on:
     types: [created]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
@@ -42,6 +44,8 @@ on:
     types: [created]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
@@ -61,6 +65,8 @@ on:
     types: [created]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
@@ -78,6 +84,8 @@ on:
     name: test-bot
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
@@ -95,6 +103,8 @@ on:
     branches: [main]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
@@ -112,6 +122,8 @@ on:
     types: [opened]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
@@ -223,6 +235,8 @@ on:
     types: [created]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
diff --git a/pkg/workflow/pr_ready_for_review_checkout_test.go b/pkg/workflow/pr_ready_for_review_checkout_test.go
index 2ce4900cb57..15008ba8cd3 100644
--- a/pkg/workflow/pr_ready_for_review_checkout_test.go
+++ b/pkg/workflow/pr_ready_for_review_checkout_test.go
@@ -22,6 +22,8 @@ on:
     types: [ready_for_review]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
@@ -38,6 +40,8 @@ on:
     types: [opened]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
@@ -54,6 +58,8 @@ on:
     branches: [main]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
@@ -150,6 +156,8 @@ on:
     types: [ready_for_review, opened]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
diff --git a/pkg/workflow/reaction_none_test.go b/pkg/workflow/reaction_none_test.go
index e63b0d4044b..10efde0a5fb 100644
--- a/pkg/workflow/reaction_none_test.go
+++ b/pkg/workflow/reaction_none_test.go
@@ -25,6 +25,8 @@ on:
   reaction: none
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 safe-outputs:
   add-comment:
@@ -108,6 +110,8 @@ on:
     name: test-bot
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 safe-outputs:
   add-comment:
@@ -193,6 +197,8 @@ on:
   reaction: rocket
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 safe-outputs:
   add-comment:
diff --git a/pkg/workflow/reaction_outputs_test.go b/pkg/workflow/reaction_outputs_test.go
index 307b9602421..bb61701f385 100644
--- a/pkg/workflow/reaction_outputs_test.go
+++ b/pkg/workflow/reaction_outputs_test.go
@@ -111,7 +111,6 @@ permissions:
   contents: read
   issues: write
   pull-requests: write
----
 
 # Test Workflow
 
diff --git a/pkg/workflow/redact_secrets_test.go b/pkg/workflow/redact_secrets_test.go
index 54f43cd27c8..cc58d445194 100644
--- a/pkg/workflow/redact_secrets_test.go
+++ b/pkg/workflow/redact_secrets_test.go
@@ -90,6 +90,8 @@ func TestSecretRedactionStepGeneration(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 ---
 
diff --git a/pkg/workflow/repository_features_validation_integration_test.go b/pkg/workflow/repository_features_validation_integration_test.go
index 24d169f2405..3f9233761cf 100644
--- a/pkg/workflow/repository_features_validation_integration_test.go
+++ b/pkg/workflow/repository_features_validation_integration_test.go
@@ -132,6 +132,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 safe-outputs:
   create-discussion:
     category: "General"
diff --git a/pkg/workflow/runtime_integration_test.go b/pkg/workflow/runtime_integration_test.go
index 55a94eb5a83..b162ae12504 100644
--- a/pkg/workflow/runtime_integration_test.go
+++ b/pkg/workflow/runtime_integration_test.go
@@ -20,6 +20,8 @@ func TestCompileWorkflowWithRuntimes(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 runtimes:
   node:
@@ -109,6 +111,8 @@ runtimes:
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 imports:
   - shared/shared-runtimes.md
@@ -195,6 +199,8 @@ func TestCompileWorkflowWithRuntimesAppliedToSteps(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 steps:
   - name: Install dependencies
@@ -251,6 +257,8 @@ func TestCompileWorkflowWithCustomActionRepo(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 steps:
   - name: Install dependencies
diff --git a/pkg/workflow/search_integration_test.go b/pkg/workflow/search_integration_test.go
index 12e2539379a..bbc9363abab 100644
--- a/pkg/workflow/search_integration_test.go
+++ b/pkg/workflow/search_integration_test.go
@@ -20,6 +20,8 @@ func TestWebSearchValidationForCopilot(t *testing.T) {
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 tools:
   web-search:
@@ -86,6 +88,8 @@ func TestWebSearchValidationForClaude(t *testing.T) {
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 tools:
   web-search:
@@ -139,6 +143,8 @@ func TestWebSearchValidationForCodex(t *testing.T) {
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: codex
 tools:
   web-search:
@@ -181,6 +187,8 @@ func TestNoWebSearchNoValidation(t *testing.T) {
 on: workflow_dispatch
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 tools:
   github:
diff --git a/pkg/workflow/source_field_test.go b/pkg/workflow/source_field_test.go
index ad17432c3d2..ee1024f3789 100644
--- a/pkg/workflow/source_field_test.go
+++ b/pkg/workflow/source_field_test.go
@@ -33,6 +33,8 @@ on:
     branches: [main]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 tools:
   github:
@@ -50,6 +52,8 @@ on:
     branches: [main]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 tools:
   github:
@@ -66,6 +70,8 @@ on:
     branches: [main]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 tools:
   github:
@@ -84,6 +90,8 @@ on:
     branches: [main]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 tools:
   github:
diff --git a/pkg/workflow/step_summary_test.go b/pkg/workflow/step_summary_test.go
index 22cdc6351a2..354ca486e74 100644
--- a/pkg/workflow/step_summary_test.go
+++ b/pkg/workflow/step_summary_test.go
@@ -21,6 +21,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues]
@@ -83,6 +84,7 @@ on: push
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues]
diff --git a/pkg/workflow/strict_mode_test.go b/pkg/workflow/strict_mode_test.go
index d81ef23ed9f..35f9eaf51ae 100644
--- a/pkg/workflow/strict_mode_test.go
+++ b/pkg/workflow/strict_mode_test.go
@@ -20,6 +20,8 @@ func TestStrictModeTimeout(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 network:
   allowed:
@@ -35,6 +37,8 @@ network:
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 timeout_minutes: 10
 engine: copilot
 network:
@@ -108,6 +112,8 @@ network:
 on: push
 permissions:
   contents: write
+  issues: read
+  pull-requests: read
 timeout_minutes: 10
 engine: copilot
 ---
@@ -203,6 +209,8 @@ network:
 on: push
 permissions:
   contents: write # NOT IN STRICT MODE
+  issues: read
+  pull-requests: read
 timeout_minutes: 10
 engine: copilot
 ---
@@ -256,6 +264,8 @@ func TestStrictModeNetwork(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 timeout_minutes: 10
 engine: copilot
 network: defaults
@@ -270,6 +280,8 @@ network: defaults
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 timeout_minutes: 10
 engine: copilot
 network:
@@ -287,6 +299,8 @@ network:
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 timeout_minutes: 10
 engine: copilot
 network:
@@ -304,6 +318,8 @@ network:
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 timeout_minutes: 10
 engine: copilot
 network: {}
@@ -357,6 +373,8 @@ func TestStrictModeMCPNetwork(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 timeout_minutes: 10
 engine: copilot
 tools:
@@ -413,6 +431,8 @@ func TestStrictModeBashTools(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 timeout_minutes: 10
 engine: copilot
 tools:
@@ -431,6 +451,8 @@ network:
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 timeout_minutes: 10
 engine: copilot
 tools:
@@ -449,6 +471,8 @@ network:
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 timeout_minutes: 10
 engine: copilot
 tools:
@@ -467,6 +491,8 @@ network:
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 timeout_minutes: 10
 engine: copilot
 tools:
@@ -486,6 +512,8 @@ network:
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 timeout_minutes: 10
 engine: copilot
 tools:
@@ -505,6 +533,8 @@ network:
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 timeout_minutes: 10
 engine: copilot
 tools:
@@ -524,6 +554,8 @@ network:
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 timeout_minutes: 10
 engine: copilot
 tools:
@@ -580,6 +612,7 @@ on: push
 permissions:
   contents: write
   issues: write
+  pull-requests: read
 engine: copilot
 network:
   allowed:
@@ -622,6 +655,8 @@ on: push
 strict: true
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 network:
   allowed:
@@ -638,6 +673,8 @@ on: push
 strict: false
 permissions:
   contents: write
+  issues: read
+  pull-requests: read
 engine: copilot
 ---
 
@@ -651,6 +688,8 @@ on: push
 strict: true
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 timeout_minutes: 10
 engine: copilot
 network:
@@ -667,6 +706,8 @@ network:
 on: push
 permissions:
   contents: write
+  issues: read
+  pull-requests: read
 engine: copilot
 ---
 
@@ -712,6 +753,8 @@ on: push
 strict: false
 permissions:
   contents: write
+  issues: read
+  pull-requests: read
 engine: copilot
 ---
 
@@ -754,6 +797,8 @@ on: push
 strict: true
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 network:
   allowed:
@@ -767,6 +812,8 @@ network:
 on: push
 permissions:
   contents: write
+  issues: read
+  pull-requests: read
 engine: copilot
 ---
 
@@ -812,6 +859,8 @@ func TestStrictModeAllowsGitHubWorkflowExpression(t *testing.T) {
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 network:
   allowed:
@@ -830,6 +879,8 @@ The workflow name is: ${{ github.workflow }}`,
 on: push
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 network:
   allowed:
@@ -847,6 +898,8 @@ Using github.workflow in a condition: ${{ github.workflow == 'my-workflow' && gi
 on: issues
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 network:
   allowed:
diff --git a/pkg/workflow/strict_mode_zizmor_test.go b/pkg/workflow/strict_mode_zizmor_test.go
index 0359818db76..998fb7d2717 100644
--- a/pkg/workflow/strict_mode_zizmor_test.go
+++ b/pkg/workflow/strict_mode_zizmor_test.go
@@ -24,6 +24,8 @@ on: push
 strict: true
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: copilot
 network:
   allowed:
diff --git a/pkg/workflow/template_expression_integration_test.go b/pkg/workflow/template_expression_integration_test.go
index 00221958599..7af7c559158 100644
--- a/pkg/workflow/template_expression_integration_test.go
+++ b/pkg/workflow/template_expression_integration_test.go
@@ -27,6 +27,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 engine: claude
 ---
 
@@ -129,6 +130,8 @@ func TestTemplateExpressionAlreadyWrapped(t *testing.T) {
 on: issues
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
@@ -192,6 +195,8 @@ func TestTemplateWithMixedExpressionsAndLiterals(t *testing.T) {
 on: issues
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
diff --git a/pkg/workflow/template_rendering_test.go b/pkg/workflow/template_rendering_test.go
index 75a6c21a14f..c580370a8e1 100644
--- a/pkg/workflow/template_rendering_test.go
+++ b/pkg/workflow/template_rendering_test.go
@@ -20,6 +20,8 @@ func TestTemplateRenderingStep(t *testing.T) {
 on: issues
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues]
@@ -125,6 +127,8 @@ func TestTemplateRenderingStepSkipped(t *testing.T) {
 on: issues
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 tools:
   edit:
   web-fetch:
@@ -182,6 +186,8 @@ func TestTemplateRenderingStepWithGitHubTool(t *testing.T) {
 on: issues
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 tools:
   github:
     allowed: [list_issues]
diff --git a/pkg/workflow/trial_issue_mode_test.go b/pkg/workflow/trial_issue_mode_test.go
index 9b3afcef4f8..f5699a23a31 100644
--- a/pkg/workflow/trial_issue_mode_test.go
+++ b/pkg/workflow/trial_issue_mode_test.go
@@ -194,6 +194,8 @@ on:
     types: [created, edited]
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 ---
 
diff --git a/pkg/workflow/trial_mode_test.go b/pkg/workflow/trial_mode_test.go
index f2800b54d0d..ccca74784dc 100644
--- a/pkg/workflow/trial_mode_test.go
+++ b/pkg/workflow/trial_mode_test.go
@@ -13,6 +13,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 safe-outputs:
   create-pull-request: {}
@@ -203,6 +205,8 @@ on:
   workflow_dispatch:
 permissions:
   contents: read
+  issues: read
+  pull-requests: read
 engine: claude
 `
 			if tc.safeOutputs != "" {
diff --git a/pkg/workflow/update_issue_test.go b/pkg/workflow/update_issue_test.go
index 7d4218fec43..45863998051 100644
--- a/pkg/workflow/update_issue_test.go
+++ b/pkg/workflow/update_issue_test.go
@@ -22,6 +22,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 engine: claude
 safe-outputs:
   update-issue:
@@ -92,6 +93,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 engine: claude
 safe-outputs:
   update-issue:
@@ -167,6 +169,7 @@ on:
 permissions:
   contents: read
   issues: write
+  pull-requests: read
 engine: claude
 safe-outputs:
   update-issue: