Send update_issue_suggestions feature flag for set_issue_fields mutation

pkg/github/__toolsnaps__/set_issue_fields.snap

@@ -4,22 +4,13 @@
     "openWorldHint": true,
     "title": "Set Issue Fields"
   },
-  "description": "Set issue field values for an issue. Fields are organization-level custom fields (text, number, date, or single select). Use this to create or update field values on an issue. When setting values, include a confidence level (low, medium, or high) reflecting how certain you are about the choice.",
+  "description": "Set issue field values for an issue. Fields are organization-level custom fields (text, number, date, or single select). Use this to create or update field values on an issue.",
   "inputSchema": {
     "properties": {
       "fields": {
         "description": "Array of issue field values to set. Each element must have a 'field_id' (string, the GraphQL node ID of the field) and exactly one value field: 'text_value' for text fields, 'number_value' for number fields, 'date_value' (ISO 8601 date string) for date fields, or 'single_select_option_id' (the GraphQL node ID of the option) for single select fields. Set 'delete' to true to remove a field value.",
         "items": {
           "properties": {
-            "confidence": {
-              "description": "How confident you are in this choice. Use 'high' for clear signal or explicit user request, 'medium' for reasonable inference with some ambiguity, 'low' for best guess with limited signal.",
-              "enum": [
-                "low",
-                "medium",
-                "high"
-              ],
-              "type": "string"
-            },
             "date_value": {
               "description": "The value to set for a date field (ISO 8601 date string)",
               "type": "string"

pkg/github/feature_flags.go

@@ -16,6 +16,13 @@ const FeatureFlagIFCLabels = "ifc_labels"
 // and field_values enrichment in list_issues / search_issues output.
 const FeatureFlagIssueFields = "remote_mcp_issue_fields"
 
+// FeatureFlagIssueConfidence is the feature flag name for exposing the
+// per-field `confidence` input on the set_issue_fields GraphQL mutation. The
+// GitHub GraphQL API does not yet accept the confidence input, so the schema
+// hides the parameter and the handler drops it from the mutation payload
+// unless this flag is enabled.
+const FeatureFlagIssueConfidence = "update_issue_confidence"
+
 // AllowedFeatureFlags is the allowlist of feature flags that can be enabled
 // by users via --features CLI flag or X-MCP-Features HTTP header.
 // Only flags in this list are accepted; unknown flags are silently ignored.
@@ -25,6 +32,7 @@ var AllowedFeatureFlags = []string{
 	FeatureFlagCSVOutput,
 	FeatureFlagIFCLabels,
 	FeatureFlagIssueFields,
+	FeatureFlagIssueConfidence,
 	FeatureFlagIssuesGranular,
 	FeatureFlagPullRequestsGranular,
 }

pkg/github/granular_tools_test.go

@@ -8,6 +8,8 @@ import (
 
 	"github.com/github/github-mcp-server/internal/githubv4mock"
 	"github.com/github/github-mcp-server/internal/toolsnaps"
+	"github.com/github/github-mcp-server/pkg/http/headers"
+	transportpkg "github.com/github/github-mcp-server/pkg/http/transport"
 	"github.com/github/github-mcp-server/pkg/inventory"
 	"github.com/github/github-mcp-server/pkg/translations"
 	gogithub "github.com/google/go-github/v87/github"
@@ -1666,7 +1668,12 @@ func TestGranularSetIssueFields(t *testing.T) {
 		}
 
 		gqlClient := githubv4.NewClient(githubv4mock.NewMockedHTTPClient(matchers...))
-		deps := BaseDeps{GQLClient: gqlClient}
+		deps := BaseDeps{
+			GQLClient: gqlClient,
+			featureChecker: func(_ context.Context, flag string) (bool, error) {
+				return flag == FeatureFlagIssueConfidence, nil
+			},
+		}
 		serverTool := GranularSetIssueFields(translations.NullTranslationHelper)
 		handler := serverTool.Handler(deps)
 
@@ -1688,7 +1695,11 @@ func TestGranularSetIssueFields(t *testing.T) {
 	})
 
 	t.Run("invalid confidence value returns error", func(t *testing.T) {
-		deps := BaseDeps{}
+		deps := BaseDeps{
+			featureChecker: func(_ context.Context, flag string) (bool, error) {
+				return flag == FeatureFlagIssueConfidence, nil
+			},
+		}
 		serverTool := GranularSetIssueFields(translations.NullTranslationHelper)
 		handler := serverTool.Handler(deps)
 
@@ -1710,6 +1721,99 @@ func TestGranularSetIssueFields(t *testing.T) {
 		assert.Contains(t, textContent.Text, "confidence must be one of: low, medium, high")
 	})
 
+	t.Run("confidence is dropped when feature flag is disabled", func(t *testing.T) {
+		matchers := []githubv4mock.Matcher{
+			githubv4mock.NewQueryMatcher(
+				struct {
+					Repository struct {
+						Issue struct {
+							ID githubv4.ID
+						} `graphql:"issue(number: $issueNumber)"`
+					} `graphql:"repository(owner: $owner, name: $repo)"`
+				}{},
+				map[string]any{
+					"owner":       githubv4.String("owner"),
+					"repo":        githubv4.String("repo"),
+					"issueNumber": githubv4.Int(5),
+				},
+				githubv4mock.DataResponse(map[string]any{
+					"repository": map[string]any{
+						"issue": map[string]any{"id": "ISSUE_123"},
+					},
+				}),
+			),
+			// Expect the mutation input WITHOUT Confidence, proving the handler
+			// dropped the user-supplied value because the feature flag is off.
+			githubv4mock.NewMutationMatcher(
+				struct {
+					SetIssueFieldValue struct {
+						Issue struct {
+							ID     githubv4.ID
+							Number githubv4.Int
+							URL    githubv4.String
+						}
+						IssueFieldValues []struct {
+							TextValue struct {
+								Value string
+							} `graphql:"... on IssueFieldTextValue"`
+							SingleSelectValue struct {
+								Name string
+							} `graphql:"... on IssueFieldSingleSelectValue"`
+							DateValue struct {
+								Value string
+							} `graphql:"... on IssueFieldDateValue"`
+							NumberValue struct {
+								Value float64
+							} `graphql:"... on IssueFieldNumberValue"`
+						}
+					} `graphql:"setIssueFieldValue(input: $input)"`
+				}{},
+				SetIssueFieldValueInput{
+					IssueID: githubv4.ID("ISSUE_123"),
+					IssueFields: []IssueFieldCreateOrUpdateInput{
+						{
+							FieldID:   githubv4.ID("FIELD_1"),
+							TextValue: githubv4.NewString(githubv4.String("hello")),
+						},
+					},
+				},
+				nil,
+				githubv4mock.DataResponse(map[string]any{
+					"setIssueFieldValue": map[string]any{
+						"issue": map[string]any{
+							"id":     "ISSUE_123",
+							"number": 5,
+							"url":    "https://github.com/owner/repo/issues/5",
+						},
+					},
+				}),
+			),
+		}
+
+		gqlClient := githubv4.NewClient(githubv4mock.NewMockedHTTPClient(matchers...))
+		deps := BaseDeps{GQLClient: gqlClient}
+		serverTool := GranularSetIssueFields(translations.NullTranslationHelper)
+		handler := serverTool.Handler(deps)
+
+		request := createMCPRequest(map[string]any{
+			"owner":        "owner",
+			"repo":         "repo",
+			"issue_number": float64(5),
+			"fields": []any{
+				map[string]any{
+					"field_id":   "FIELD_1",
+					"text_value": "hello",
+					// Confidence is supplied but should be silently dropped
+					// because FeatureFlagIssueConfidence is off.
+					"confidence": "high",
+				},
+			},
+		})
+		result, err := handler(ContextWithDeps(context.Background(), deps), &request)
+		require.NoError(t, err)
+		assert.False(t, result.IsError, getTextResult(t, result).Text)
+	})
+
 	t.Run("successful set with suggest flag", func(t *testing.T) {
 		suggestTrue := githubv4.Boolean(true)
 		matchers := []githubv4mock.Matcher{
@@ -1802,4 +1906,101 @@ func TestGranularSetIssueFields(t *testing.T) {
 		require.NoError(t, err)
 		assert.False(t, result.IsError)
 	})
+
+	t.Run("sends GraphQL-Features: update_issue_suggestions header on mutation", func(t *testing.T) {
+		matchers := []githubv4mock.Matcher{
+			githubv4mock.NewQueryMatcher(
+				struct {
+					Repository struct {
+						Issue struct {
+							ID githubv4.ID
+						} `graphql:"issue(number: $issueNumber)"`
+					} `graphql:"repository(owner: $owner, name: $repo)"`
+				}{},
+				map[string]any{
+					"owner":       githubv4.String("owner"),
+					"repo":        githubv4.String("repo"),
+					"issueNumber": githubv4.Int(5),
+				},
+				githubv4mock.DataResponse(map[string]any{
+					"repository": map[string]any{
+						"issue": map[string]any{"id": "ISSUE_123"},
+					},
+				}),
+			),
+			githubv4mock.NewMutationMatcher(
+				struct {
+					SetIssueFieldValue struct {
+						Issue struct {
+							ID     githubv4.ID
+							Number githubv4.Int
+							URL    githubv4.String
+						}
+						IssueFieldValues []struct {
+							TextValue struct {
+								Value string
+							} `graphql:"... on IssueFieldTextValue"`
+							SingleSelectValue struct {
+								Name string
+							} `graphql:"... on IssueFieldSingleSelectValue"`
+							DateValue struct {
+								Value string
+							} `graphql:"... on IssueFieldDateValue"`
+							NumberValue struct {
+								Value float64
+							} `graphql:"... on IssueFieldNumberValue"`
+						}
+					} `graphql:"setIssueFieldValue(input: $input)"`
+				}{},
+				SetIssueFieldValueInput{
+					IssueID: githubv4.ID("ISSUE_123"),
+					IssueFields: []IssueFieldCreateOrUpdateInput{
+						{
+							FieldID:   githubv4.ID("FIELD_1"),
+							TextValue: githubv4.NewString(githubv4.String("hello")),
+						},
+					},
+				},
+				nil,
+				githubv4mock.DataResponse(map[string]any{
+					"setIssueFieldValue": map[string]any{
+						"issue": map[string]any{
+							"id":     "ISSUE_123",
+							"number": 5,
+							"url":    "https://github.com/owner/repo/issues/5",
+						},
+					},
+				}),
+			),
+		}
+
+		// Build a transport chain matching production: GraphQLFeaturesTransport
+		// wraps a header-capturing spy, which forwards to the mock's RoundTripper.
+		// This verifies the mutation request sets the update_issue_suggestions
+		// feature flag so the rationale/suggest input fields are accepted.
+		mockClient := githubv4mock.NewMockedHTTPClient(matchers...)
+		spy := &headerCaptureTransport{inner: mockClient.Transport}
+		httpClient := &http.Client{
+			Transport: &transportpkg.GraphQLFeaturesTransport{Transport: spy},
+		}
+		gqlClient := githubv4.NewClient(httpClient)
+		deps := BaseDeps{GQLClient: gqlClient}
+		serverTool := GranularSetIssueFields(translations.NullTranslationHelper)
+		handler := serverTool.Handler(deps)
+
+		request := createMCPRequest(map[string]any{
+			"owner":        "owner",
+			"repo":         "repo",
+			"issue_number": float64(5),
+			"fields": []any{
+				map[string]any{"field_id": "FIELD_1", "text_value": "hello"},
+			},
+		})
+		result, err := handler(ContextWithDeps(context.Background(), deps), &request)
+		require.NoError(t, err)
+		require.False(t, result.IsError, getTextResult(t, result).Text)
+		// The last request captured is the mutation; the preceding issue ID
+		// query does not require the feature flag.
+		assert.Equal(t, "update_issue_suggestions", spy.captured.Get(headers.GraphQLFeaturesHeader))
+	})
 }

pkg/github/issues_granular.go

@@ -7,6 +7,7 @@ import (
 	"maps"
 	"strings"
 
+	ghcontext "github.com/github/github-mcp-server/pkg/context"
 	ghErrors "github.com/github/github-mcp-server/pkg/errors"
 	"github.com/github/github-mcp-server/pkg/inventory"
 	"github.com/github/github-mcp-server/pkg/scopes"
@@ -924,7 +925,7 @@ func GranularSetIssueFields(t translations.TranslationHelperFunc) inventory.Serv
 		ToolsetMetadataIssues,
 		mcp.Tool{
 			Name:        "set_issue_fields",
-			Description: t("TOOL_SET_ISSUE_FIELDS_DESCRIPTION", "Set issue field values for an issue. Fields are organization-level custom fields (text, number, date, or single select). Use this to create or update field values on an issue. When setting values, include a confidence level (low, medium, or high) reflecting how certain you are about the choice."),
+			Description: t("TOOL_SET_ISSUE_FIELDS_DESCRIPTION", "Set issue field values for an issue. Fields are organization-level custom fields (text, number, date, or single select). Use this to create or update field values on an issue."),
 			Annotations: &mcp.ToolAnnotations{
 				Title:           t("TOOL_SET_ISSUE_FIELDS_USER_TITLE", "Set Issue Fields"),
 				ReadOnlyHint:    false,
@@ -984,11 +985,6 @@ func GranularSetIssueFields(t translations.TranslationHelperFunc) inventory.Serv
 										"State the concrete signal (e.g. 'Reports a crash when saving' → high priority).",
 									MaxLength: jsonschema.Ptr(280),
 								},
-								"confidence": {
-									Type:        "string",
-									Description: "How confident you are in this choice. Use 'high' for clear signal or explicit user request, 'medium' for reasonable inference with some ambiguity, 'low' for best guess with limited signal.",
-									Enum:        []any{"low", "medium", "high"},
-								},
 								"is_suggestion": {
 									Type: "boolean",
 									Description: "If true, this field value is sent to the API as a suggestion (suggest:true) rather than an applied value. " +
@@ -1106,15 +1102,21 @@ func GranularSetIssueFields(t translations.TranslationHelperFunc) inventory.Serv
 					}
 				}
 
-				confidence, err := OptionalParam[string](fieldMap, "confidence")
-				if err != nil {
-					return utils.NewToolResultError(err.Error()), nil, nil
-				}
-				if confidence != "" && confidence != "low" && confidence != "medium" && confidence != "high" {
-					return utils.NewToolResultError("confidence must be one of: low, medium, high"), nil, nil
-				}
-				if confidence != "" {
-					input.Confidence = &confidence
+				// The `confidence` input is gated behind FeatureFlagIssueConfidence
+				// because the GitHub GraphQL API does not yet accept it. When the
+				// flag is off the schema hides the field and the handler drops
+				// any value supplied by older callers from the mutation payload.
+				if deps.IsFeatureEnabled(ctx, FeatureFlagIssueConfidence) {
+					confidence, err := OptionalParam[string](fieldMap, "confidence")
+					if err != nil {
+						return utils.NewToolResultError(err.Error()), nil, nil
+					}
+					if confidence != "" && confidence != "low" && confidence != "medium" && confidence != "high" {
+						return utils.NewToolResultError("confidence must be one of: low, medium, high"), nil, nil
+					}
+					if confidence != "" {
+						input.Confidence = &confidence
+					}
 				}
 
 				isSuggestion, err := OptionalParam[bool](fieldMap, "is_suggestion")
@@ -1170,7 +1172,10 @@ func GranularSetIssueFields(t translations.TranslationHelperFunc) inventory.Serv
 				IssueFields: issueFields,
 			}
 
-			if err := gqlClient.Mutate(ctx, &mutation, mutationInput, nil); err != nil {
+			// The rationale and suggest input fields on IssueFieldCreateOrUpdateInput
+			// are gated behind the update_issue_suggestions GraphQL feature flag.
+			ctxWithFeatures := ghcontext.WithGraphQLFeatures(ctx, "update_issue_suggestions")
+			if err := gqlClient.Mutate(ctxWithFeatures, &mutation, mutationInput, nil); err != nil {
 				return ghErrors.NewGitHubGraphQLErrorResponse(ctx, "failed to set issue field values", err), nil, nil
 			}