Add ConnectIssueGraph prompt for finding and connecting missing issue/PR relationships

This prompt provides a guided workflow for:
1. Running issue_graph to see current state
2. Searching for related issues/PRs that should be connected
3. Identifying orphaned or missing relationships
4. Proposing and adding connections with user approval
5. Verifying connections via issue_graph

Parameters:
- owner/repo/issue_number: The issue/PR to analyze
- additional_repos: Cross-repo search (e.g., epic in planning repo)
- known_links: User-provided issue URLs that should be connected

Author: SamMorrowDrums

pkg/github/issue_graph.go

@@ -110,10 +110,27 @@ var (
 	whitespaceRegex = regexp.MustCompile(`\s+`)
 	// HTML tags to remove
 	htmlTagRegex = regexp.MustCompile(`<[^>]*>`)
+	// Code block patterns to remove before extracting references
+	fencedCodeBlockRegex = regexp.MustCompile("(?s)```[^`]*```")
+	inlineCodeRegex      = regexp.MustCompile("`[^`]+`")
 )
 
+// stripCodeBlocks removes fenced code blocks and inline code from text
+// This prevents extracting issue references from example code
+func stripCodeBlocks(text string) string {
+	// Remove fenced code blocks first (```...```)
+	text = fencedCodeBlockRegex.ReplaceAllString(text, "")
+	// Remove inline code (`...`)
+	text = inlineCodeRegex.ReplaceAllString(text, "")
+	return text
+}
+
 // extractIssueReferences extracts all issue/PR references from text
+// It strips code blocks first to avoid picking up example references
 func extractIssueReferences(text, defaultOwner, defaultRepo string) []IssueReference {
+	// Strip code blocks to avoid extracting references from examples
+	text = stripCodeBlocks(text)
+
 	refs := make([]IssueReference, 0)
 	seen := make(map[string]bool)
 
@@ -495,6 +512,11 @@ func (gc *graphCrawler) crawl(ctx context.Context) error {
 
 			refKey := nodeKey(ref.Owner, ref.Repo, ref.Number)
 
+			// Skip self-references
+			if refKey == key {
+				continue
+			}
+
 			// Determine relationship
 			relType := RelationTypeRelated
 			if ref.IsParent {
@@ -629,6 +651,14 @@ func (gc *graphCrawler) crawl(ctx context.Context) error {
 	return nil
 }
 
+// edgeKey creates a unique key for an edge to enable deduplication
+func edgeKey(e GraphEdge) string {
+	return fmt.Sprintf("%s/%s#%d->%s/%s#%d:%s",
+		strings.ToLower(e.FromOwner), strings.ToLower(e.FromRepo), e.FromNumber,
+		strings.ToLower(e.ToOwner), strings.ToLower(e.ToRepo), e.ToNumber,
+		e.Relation)
+}
+
 // buildGraph constructs the final IssueGraph
 func (gc *graphCrawler) buildGraph() *IssueGraph {
 	gc.mu.RLock()
@@ -648,12 +678,23 @@ func (gc *graphCrawler) buildGraph() *IssueGraph {
 		return nodes[i].Number < nodes[j].Number
 	})
 
+	// Deduplicate edges
+	seenEdges := make(map[string]bool)
+	uniqueEdges := make([]GraphEdge, 0, len(gc.edges))
+	for _, edge := range gc.edges {
+		key := edgeKey(edge)
+		if !seenEdges[key] {
+			seenEdges[key] = true
+			uniqueEdges = append(uniqueEdges, edge)
+		}
+	}
+
 	return &IssueGraph{
 		FocusOwner:  gc.focusOwner,
 		FocusRepo:   gc.focusRepo,
 		FocusNumber: gc.focusNumber,
 		Nodes:       nodes,
-		Edges:       gc.edges,
+		Edges:       uniqueEdges,
 		Summary:     gc.generateSummary(),
 	}
 }

pkg/github/issue_graph_prompts.go

@@ -0,0 +1,136 @@
+package github
+
+import (
+	"context"
+	"fmt"
+
+	"github.com/github/github-mcp-server/pkg/translations"
+	"github.com/mark3labs/mcp-go/mcp"
+	"github.com/mark3labs/mcp-go/server"
+)
+
+// ConnectIssueGraphPrompt provides a guided workflow for finding and connecting missing relationships
+// between issues and PRs in the issue graph
+func ConnectIssueGraphPrompt(t translations.TranslationHelperFunc) (tool mcp.Prompt, handler server.PromptHandlerFunc) {
+	return mcp.NewPrompt("ConnectIssueGraph",
+			mcp.WithPromptDescription(t("PROMPT_CONNECT_ISSUE_GRAPH_DESCRIPTION", "Find and connect missing relationships between issues and PRs in the issue graph")),
+			mcp.WithArgument("owner", mcp.ArgumentDescription("Repository owner"), mcp.RequiredArgument()),
+			mcp.WithArgument("repo", mcp.ArgumentDescription("Repository name"), mcp.RequiredArgument()),
+			mcp.WithArgument("issue_number", mcp.ArgumentDescription("Issue or PR number to analyze"), mcp.RequiredArgument()),
+			mcp.WithArgument("additional_repos", mcp.ArgumentDescription("Comma-separated list of additional owner/repo to search (e.g., 'github/copilot,microsoft/vscode')")),
+			mcp.WithArgument("known_links", mcp.ArgumentDescription("Comma-separated list of known related issue URLs that should be connected (e.g., epic links in other repos)")),
+		), func(_ context.Context, request mcp.GetPromptRequest) (*mcp.GetPromptResult, error) {
+			owner := request.Params.Arguments["owner"]
+			repo := request.Params.Arguments["repo"]
+			issueNumber := request.Params.Arguments["issue_number"]
+
+			additionalRepos := ""
+			if r, exists := request.Params.Arguments["additional_repos"]; exists {
+				additionalRepos = fmt.Sprintf("%v", r)
+			}
+
+			knownLinks := ""
+			if k, exists := request.Params.Arguments["known_links"]; exists {
+				knownLinks = fmt.Sprintf("%v", k)
+			}
+
+			systemPrompt := `You are a GitHub issue graph connection assistant. Your job is to find missing relationships between issues and PRs and help connect them properly.
+
+WORKFLOW:
+1. First, use issue_graph tool on the specified issue/PR to see current relationships
+2. Search for potentially related issues and PRs using search_issues and search_pull_requests
+3. Identify missing connections (orphaned tasks, PRs without issue links, etc.)
+4. For each missing connection, help the user add the appropriate reference
+5. Verify the connections by running issue_graph again
+
+RELATIONSHIP TYPES TO LOOK FOR:
+- Epic → Batch: Large initiatives broken into batches
+- Batch → Task: Parent issues with sub-issues
+- Task → PR: Issues with PRs that should "close" them
+- Cross-repo: Epics/batches in different repos (e.g., planning repo vs implementation repo)
+
+SEARCH STRATEGIES:
+- Search by keywords from the issue title
+- Search by feature name or component
+- Look for PRs that mention the issue number
+- Check for issues with similar labels
+
+ADDING CONNECTIONS:
+- PRs should reference issues with "Closes #123" or "Fixes #123" in body
+- Cross-repo: "Closes owner/repo#123"
+- Sub-issues can be added via the sub_issue_write tool
+- Issue bodies can reference related work with "Related to #123"
+
+IMPORTANT:
+- Ask the user before making any changes
+- Cross-repo epics may need user input (they might not be searchable)
+- Some relationships are intentionally loose - confirm with user`
+
+			userPrompt := fmt.Sprintf(`I want to analyze and connect the issue graph for %s/%s#%s.
+
+Please:
+1. Run issue_graph on this issue/PR to see current state
+2. Search for related issues and PRs that should be connected
+3. Identify any orphaned or missing relationships
+4. Propose specific connections to add
+5. After I approve changes, help me add the connections
+6. Verify by running issue_graph again`, owner, repo, issueNumber)
+
+			if additionalRepos != "" {
+				userPrompt += fmt.Sprintf(`
+
+Also search these additional repositories for related issues/PRs:
+%s`, additionalRepos)
+			}
+
+			if knownLinks != "" {
+				userPrompt += fmt.Sprintf(`
+
+These are known related issues that should be connected (e.g., epics in other repos):
+%s
+
+Please verify these are properly referenced and suggest how to connect them if not.`, knownLinks)
+			}
+
+			messages := []mcp.PromptMessage{
+				{
+					Role:    "user",
+					Content: mcp.NewTextContent(systemPrompt),
+				},
+				{
+					Role:    "user",
+					Content: mcp.NewTextContent(userPrompt),
+				},
+				{
+					Role: "assistant",
+					Content: mcp.NewTextContent(fmt.Sprintf(`I'll help you analyze and connect the issue graph for %s/%s#%s.
+
+Let me start by running the issue_graph tool to see the current state of relationships:
+
+**Step 1: Analyze Current Graph**
+I'll call issue_graph to see what connections already exist.
+
+**Step 2: Search for Missing Connections**
+Then I'll search for:
+- PRs that might close this issue but don't reference it
+- Related issues that should be sub-issues or parent issues
+- Cross-repo references that might be missing
+
+**Step 3: Propose Connections**
+I'll list any missing relationships I find and propose how to connect them.
+
+**Step 4: Make Changes (with your approval)**
+After you review, I'll help add the connections.
+
+**Step 5: Verify**
+Finally, I'll run issue_graph again to confirm the connections.
+
+Let me start by getting the current issue graph...`, owner, repo, issueNumber)),
+				},
+			}
+
+			return &mcp.GetPromptResult{
+				Messages: messages,
+			}, nil
+		}
+}

pkg/github/tools.go

@@ -215,6 +215,7 @@ func DefaultToolsetGroup(readOnly bool, getClient GetClientFn, getGQLClient GetG
 		).AddPrompts(
 		toolsets.NewServerPrompt(AssignCodingAgentPrompt(t)),
 		toolsets.NewServerPrompt(IssueToFixWorkflowPrompt(t)),
+		toolsets.NewServerPrompt(ConnectIssueGraphPrompt(t)),
 	)
 	users := toolsets.NewToolset(ToolsetMetadataUsers.ID, ToolsetMetadataUsers.Description).
 		AddReadTools(