Fix delete:true on issue fields by calling deleteIssueFieldValue mutation

The REST update endpoint uses set semantics for issue_field_values:
sending {"issue_field_values": [...]} overwrites the entire list. We
were relying on that to clear deleted fields by omitting them from the
merged payload, but Go's omitempty strips an empty
[]*IssueRequestFieldValue from the JSON, so when the kept list ended up
empty (e.g. deleting the only remaining field value) nothing got sent
and the field kept its old value.

Capture each field's GraphQL node ID alongside its database ID at
resolve time, and after the REST PATCH succeeds run
deleteIssueFieldValue per deletion. The GraphQL mutation is idempotent,
per-field, and not subject to the omitempty silent-no-op. It also
sidesteps the race window in the old fetch-merge-PATCH approach (where
a concurrent edit between our fetch and our PATCH would be silently
clobbered by the set semantics).

Verified end-to-end:

- Test_IssueRequest_EmptyFieldValues_OmittedByJSON pins the omitempty
  contract so we know if go-github ever drops the tag.

- Test_UpdateIssue_DeleteFieldValueRunsGraphQLMutation deletes the only
  existing field value, captures the REST PATCH body, asserts it has no
  issue_field_values key, and asserts (via mutation matcher) that the
  GraphQL clear fires.

- Test_UpdateIssue_DeleteAndSetFieldsInSameCall does a combined
  set-one-delete-another in a single call and verifies the REST PATCH
  carries only the set operation while the GraphQL mutation fires for
  the deletion.

Empirical confirmation of the bug on main (pre-fix): running an
equivalent flow there results in a literal PATCH body of '{}' and no
follow-up mutation — the field is never cleared on the server.

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: owenniblock

pkg/github/issues.go

@@ -121,21 +121,25 @@ func getCloseStateReason(stateReason string) IssueClosedStateReason {
 type issueFieldWriteMetadataNode struct {
 	TypeName       githubv4.String `graphql:"__typename"`
 	IssueFieldText struct {
+		ID             githubv4.ID
 		FullDatabaseID githubv4.String `graphql:"fullDatabaseId"`
 		Name           githubv4.String
 		DataType       githubv4.String
 	} `graphql:"... on IssueFieldText"`
 	IssueFieldNumber struct {
+		ID             githubv4.ID
 		FullDatabaseID githubv4.String `graphql:"fullDatabaseId"`
 		Name           githubv4.String
 		DataType       githubv4.String
 	} `graphql:"... on IssueFieldNumber"`
 	IssueFieldDate struct {
+		ID             githubv4.ID
 		FullDatabaseID githubv4.String `graphql:"fullDatabaseId"`
 		Name           githubv4.String
 		DataType       githubv4.String
 	} `graphql:"... on IssueFieldDate"`
 	IssueFieldSingleSelect struct {
+		ID             githubv4.ID
 		FullDatabaseID githubv4.String `graphql:"fullDatabaseId"`
 		Name           githubv4.String
 		DataType       githubv4.String
@@ -299,7 +303,15 @@ func optionalIssueWriteFields(args map[string]any) ([]issueWriteFieldInput, erro
 	return issueFields, nil
 }
 
-func resolveIssueRequestFieldValues(ctx context.Context, gqlClient *githubv4.Client, owner, repo string, issueFields []issueWriteFieldInput) ([]*github.IssueRequestFieldValue, []int64, error) {
+// fieldDeletion carries both identifiers needed to clear an issue field value:
+// the REST/v3 database ID (used to exclude the field from the REST PATCH payload)
+// and the GraphQL node ID (used as input to the deleteIssueFieldValue mutation).
+type fieldDeletion struct {
+	DatabaseID int64
+	NodeID     githubv4.ID
+}
+
+func resolveIssueRequestFieldValues(ctx context.Context, gqlClient *githubv4.Client, owner, repo string, issueFields []issueWriteFieldInput) ([]*github.IssueRequestFieldValue, []fieldDeletion, error) {
 	if len(issueFields) == 0 {
 		return nil, nil, nil
 	}
@@ -334,27 +346,32 @@ func resolveIssueRequestFieldValues(ctx context.Context, gqlClient *githubv4.Cli
 	}
 
 	resolved := make([]*github.IssueRequestFieldValue, 0, len(issueFields))
-	var fieldIDsToDelete []int64
+	var fieldsToDelete []fieldDeletion
 	for _, fieldInput := range issueFields {
 		node, ok := fieldByName[strings.ToLower(strings.TrimSpace(fieldInput.FieldName))]
 		if !ok {
 			return nil, nil, fmt.Errorf("issue field %q was not found in %s/%s", fieldInput.FieldName, owner, repo)
 		}
 
 		var fullDatabaseIDStr, dataType string
+		var nodeID githubv4.ID
 		switch string(node.TypeName) {
 		case "IssueFieldText":
 			fullDatabaseIDStr = string(node.IssueFieldText.FullDatabaseID)
 			dataType = string(node.IssueFieldText.DataType)
+			nodeID = node.IssueFieldText.ID
 		case "IssueFieldNumber":
 			fullDatabaseIDStr = string(node.IssueFieldNumber.FullDatabaseID)
 			dataType = string(node.IssueFieldNumber.DataType)
+			nodeID = node.IssueFieldNumber.ID
 		case "IssueFieldDate":
 			fullDatabaseIDStr = string(node.IssueFieldDate.FullDatabaseID)
 			dataType = string(node.IssueFieldDate.DataType)
+			nodeID = node.IssueFieldDate.ID
 		case "IssueFieldSingleSelect":
 			fullDatabaseIDStr = string(node.IssueFieldSingleSelect.FullDatabaseID)
 			dataType = string(node.IssueFieldSingleSelect.DataType)
+			nodeID = node.IssueFieldSingleSelect.ID
 		}
 
 		fieldID := parseFullDatabaseID(fullDatabaseIDStr)
@@ -363,7 +380,7 @@ func resolveIssueRequestFieldValues(ctx context.Context, gqlClient *githubv4.Cli
 		}
 
 		if fieldInput.Delete {
-			fieldIDsToDelete = append(fieldIDsToDelete, fieldID)
+			fieldsToDelete = append(fieldsToDelete, fieldDeletion{DatabaseID: fieldID, NodeID: nodeID})
 			continue
 		}
 
@@ -394,7 +411,7 @@ func resolveIssueRequestFieldValues(ctx context.Context, gqlClient *githubv4.Cli
 		})
 	}
 
-	return resolved, fieldIDsToDelete, nil
+	return resolved, fieldsToDelete, nil
 }
 
 // fetchExistingIssueFieldValues retrieves the current field values for an issue
@@ -1999,9 +2016,9 @@ Options are:
 			}
 
 			var issueFieldValues []*github.IssueRequestFieldValue
-			var fieldIDsToDelete []int64
+			var fieldsToDelete []fieldDeletion
 			if len(issueFields) > 0 {
-				issueFieldValues, fieldIDsToDelete, err = resolveIssueRequestFieldValues(ctx, gqlClient, owner, repo, issueFields)
+				issueFieldValues, fieldsToDelete, err = resolveIssueRequestFieldValues(ctx, gqlClient, owner, repo, issueFields)
 				if err != nil {
 					return utils.NewToolResultError(fmt.Sprintf("failed to resolve issue_fields: %v", err)), nil, nil
 				}
@@ -2016,7 +2033,7 @@ Options are:
 				if err != nil {
 					return utils.NewToolResultError(err.Error()), nil, nil
 				}
-				result, err := UpdateIssue(ctx, client, gqlClient, owner, repo, issueNumber, title, body, assignees, labels, milestoneNum, issueType, issueFieldValues, fieldIDsToDelete, state, stateReason, duplicateOf, UpdateIssueOptions{
+				result, err := UpdateIssue(ctx, client, gqlClient, owner, repo, issueNumber, title, body, assignees, labels, milestoneNum, issueType, issueFieldValues, fieldsToDelete, state, stateReason, duplicateOf, UpdateIssueOptions{
 					AssigneesProvided: assigneesProvided,
 					LabelsProvided:    labelsProvided,
 				})
@@ -2091,7 +2108,7 @@ type UpdateIssueOptions struct {
 	LabelsProvided bool
 }
 
-func UpdateIssue(ctx context.Context, client *github.Client, gqlClient *githubv4.Client, owner string, repo string, issueNumber int, title string, body string, assignees []string, labels []string, milestoneNum int, issueType string, issueFieldValues []*github.IssueRequestFieldValue, fieldIDsToDelete []int64, state string, stateReason string, duplicateOf int, opts ...UpdateIssueOptions) (*mcp.CallToolResult, error) {
+func UpdateIssue(ctx context.Context, client *github.Client, gqlClient *githubv4.Client, owner string, repo string, issueNumber int, title string, body string, assignees []string, labels []string, milestoneNum int, issueType string, issueFieldValues []*github.IssueRequestFieldValue, fieldsToDelete []fieldDeletion, state string, stateReason string, duplicateOf int, opts ...UpdateIssueOptions) (*mcp.CallToolResult, error) {
 	updateOptions := UpdateIssueOptions{
 		AssigneesProvided: len(assignees) > 0,
 		LabelsProvided:    len(labels) > 0,
@@ -2129,19 +2146,23 @@ func UpdateIssue(ctx context.Context, client *github.Client, gqlClient *githubv4
 		issueRequest.Type = github.Ptr(issueType)
 	}
 
-	if len(issueFieldValues) > 0 || len(fieldIDsToDelete) > 0 {
+	if len(issueFieldValues) > 0 {
 		// The REST update endpoint uses "set" semantics — it overwrites all existing
-		// field values with whatever is sent. Fetch the current values first, merge in
-		// the new values, then remove any explicitly deleted fields.
+		// field values with whatever is sent. Fetch the current values first and
+		// merge the new values on top so untouched fields survive. Anything marked
+		// for deletion is NOT included in the REST payload (the REST PATCH can't
+		// clear values — Go's `omitempty` strips an empty issue_field_values array
+		// from the JSON, so even sending the cleared list is a silent no-op); we
+		// follow up with deleteIssueFieldValue GraphQL mutations below.
 		existing, err := fetchExistingIssueFieldValues(ctx, gqlClient, owner, repo, issueNumber)
 		if err != nil {
 			return ghErrors.NewGitHubGraphQLErrorResponse(ctx, "failed to fetch existing issue field values", err), nil
 		}
 		merged := mergeIssueFieldValues(existing, issueFieldValues)
-		if len(fieldIDsToDelete) > 0 {
-			deleteSet := make(map[int64]bool, len(fieldIDsToDelete))
-			for _, id := range fieldIDsToDelete {
-				deleteSet[id] = true
+		if len(fieldsToDelete) > 0 {
+			deleteSet := make(map[int64]bool, len(fieldsToDelete))
+			for _, d := range fieldsToDelete {
+				deleteSet[d.DatabaseID] = true
 			}
 			kept := make([]*github.IssueRequestFieldValue, 0, len(merged))
 			for _, v := range merged {
@@ -2172,6 +2193,33 @@ func UpdateIssue(ctx context.Context, client *github.Client, gqlClient *githubv4
 		return ghErrors.NewGitHubAPIStatusErrorResponse(ctx, "failed to update issue", resp, body), nil
 	}
 
+	// Clear any fields marked with delete:true via the GraphQL deleteIssueFieldValue
+	// mutation. REST alone can't do this — sending an empty `issue_field_values: []`
+	// would be stripped by omitempty before reaching the server. One mutation per
+	// deleted field; failures bubble up immediately so callers see the first error.
+	if len(fieldsToDelete) > 0 {
+		issueID, _, err := fetchIssueIDs(ctx, gqlClient, owner, repo, issueNumber, 0)
+		if err != nil {
+			return ghErrors.NewGitHubGraphQLErrorResponse(ctx, "failed to look up issue for field deletion", err), nil
+		}
+		for _, deletion := range fieldsToDelete {
+			var mutation struct {
+				DeleteIssueFieldValue struct {
+					Issue struct {
+						Number githubv4.Int
+					}
+				} `graphql:"deleteIssueFieldValue(input: $input)"`
+			}
+			input := DeleteIssueFieldValueInput{
+				IssueID: issueID,
+				FieldID: deletion.NodeID,
+			}
+			if err := gqlClient.Mutate(ctx, &mutation, input, nil); err != nil {
+				return ghErrors.NewGitHubGraphQLErrorResponse(ctx, "failed to clear issue field value", err), nil
+			}
+		}
+	}
+
 	// Use GraphQL API for state updates
 	if state != "" {
 		// Mandate specifying duplicateOf when trying to close as duplicate