feat: add package indexing to MCP index_revision tool

The options server's index_revision now also indexes packages when running
under nixpkgs-search, matching the CLI behavior. The packages server gets
its own index_revision tool for standalone package indexing.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

CLAUDE.md

@@ -144,7 +144,7 @@ labmcp/
 | `search_options` | Full-text search across option names and descriptions |
 | `get_option` | Get full details for a specific option with children |
 | `get_file` | Fetch source file contents from indexed repository |
-| `index_revision` | Index a revision (by hash or channel name) |
+| `index_revision` | Index a revision (options, files, and packages for nixpkgs) |
 | `list_revisions` | List all indexed revisions |
 | `delete_revision` | Delete an indexed revision |
 
@@ -155,6 +155,7 @@ labmcp/
 | `search_packages` | Full-text search across package names and descriptions |
 | `get_package` | Get full details for a specific package by attr path |
 | `get_file` | Fetch source file contents from nixpkgs |
+| `index_revision` | Index a revision to make its packages searchable |
 | `list_revisions` | List all indexed revisions |
 | `delete_revision` | Delete an indexed revision |
 

README.md

@@ -384,7 +384,7 @@ hm-options -d "sqlite://my.db" index hm-unstable
 | `search_options` | Search for options by name or description |
 | `get_option` | Get full details for a specific option |
 | `get_file` | Fetch source file contents from the repository |
-| `index_revision` | Index a revision |
+| `index_revision` | Index a revision (options, files, and packages for nixpkgs) |
 | `list_revisions` | List all indexed revisions |
 | `delete_revision` | Delete an indexed revision |
 
@@ -395,7 +395,7 @@ hm-options -d "sqlite://my.db" index hm-unstable
 | `search_packages` | Search for packages by name or description |
 | `get_package` | Get full details for a specific package |
 | `get_file` | Fetch source file contents from nixpkgs |
-| `index_revision` | Index a revision |
+| `index_revision` | Index a revision to make its packages searchable |
 | `list_revisions` | List all indexed revisions |
 | `delete_revision` | Delete an indexed revision |
 

cmd/nixpkgs-search/main.go

@@ -20,7 +20,7 @@ import (
 
 const (
 	defaultDatabase = "sqlite://nixpkgs-search.db"
-	version         = "0.3.0"
+	version         = "0.4.0"
 )
 
 func main() {
@@ -310,7 +310,8 @@ func runOptionsServe(c *cli.Context) error {
 	server := mcp.NewServer(store, logger, config)
 
 	indexer := nixos.NewIndexer(store)
-	server.RegisterHandlers(indexer)
+	pkgIndexer := packages.NewIndexer(store)
+	server.RegisterHandlersWithPackages(indexer, pkgIndexer)
 
 	transport := c.String("transport")
 	switch transport {

internal/mcp/handlers.go

@@ -14,12 +14,29 @@ import (
 )
 
 // RegisterHandlers registers all tool handlers on the server for options mode.
+// Used by legacy nixos-options and hm-options servers (no package indexing).
 func (s *Server) RegisterHandlers(indexer options.Indexer) {
+	s.registerOptionsHandlers(indexer, nil)
+}
+
+// RegisterHandlersWithPackages registers all tool handlers for options mode
+// with additional package indexing support. When pkgIndexer is non-nil,
+// index_revision will also index packages, and list_revisions will show package counts.
+func (s *Server) RegisterHandlersWithPackages(indexer options.Indexer, pkgIndexer *packages.Indexer) {
+	s.registerOptionsHandlers(indexer, pkgIndexer)
+}
+
+// registerOptionsHandlers is the shared implementation for RegisterHandlers and RegisterHandlersWithPackages.
+func (s *Server) registerOptionsHandlers(indexer options.Indexer, pkgIndexer *packages.Indexer) {
 	s.tools["search_options"] = s.handleSearchOptions
 	s.tools["get_option"] = s.handleGetOption
 	s.tools["get_file"] = s.handleGetFile
-	s.tools["index_revision"] = s.makeIndexHandler(indexer)
+	s.tools["index_revision"] = s.makeIndexHandler(indexer, pkgIndexer)
+	if pkgIndexer != nil {
+		s.tools["list_revisions"] = s.handleListRevisionsWithPackages
+	} else {
 		s.tools["list_revisions"] = s.handleListRevisions
+	}
 	s.tools["delete_revision"] = s.handleDeleteRevision
 }
 
@@ -28,6 +45,7 @@ func (s *Server) RegisterPackageHandlers(pkgIndexer *packages.Indexer) {
 	s.tools["search_packages"] = s.handleSearchPackages
 	s.tools["get_package"] = s.handleGetPackage
 	s.tools["get_file"] = s.handleGetFile
+	s.tools["index_revision"] = s.makePackageIndexHandler(pkgIndexer)
 	s.tools["list_revisions"] = s.handleListRevisionsWithPackages
 	s.tools["delete_revision"] = s.handleDeleteRevision
 }
@@ -246,7 +264,8 @@ func (s *Server) handleGetFile(ctx context.Context, args map[string]interface{})
 }
 
 // makeIndexHandler creates the index_revision handler with the indexer.
-func (s *Server) makeIndexHandler(indexer options.Indexer) ToolHandler {
+// If pkgIndexer is non-nil, it will also index packages after options and files.
+func (s *Server) makeIndexHandler(indexer options.Indexer, pkgIndexer *packages.Indexer) ToolHandler {
 	return func(ctx context.Context, args map[string]interface{}) (CallToolResult, error) {
 		revision, _ := args["revision"].(string)
 		if revision == "" {
@@ -278,6 +297,17 @@ func (s *Server) makeIndexHandler(indexer options.Indexer) ToolHandler {
 			s.logger.Printf("Warning: file indexing failed: %v", err)
 		}
 
+		// Index packages if package indexer is available
+		var packageCount int
+		if pkgIndexer != nil {
+			pkgResult, pkgErr := pkgIndexer.IndexPackages(ctx, result.Revision.ID, result.Revision.GitHash)
+			if pkgErr != nil {
+				s.logger.Printf("Warning: package indexing failed: %v", pkgErr)
+			} else {
+				packageCount = pkgResult.PackageCount
+			}
+		}
+
 		var sb strings.Builder
 		sb.WriteString(fmt.Sprintf("Indexed revision: %s\n", result.Revision.GitHash))
 		if result.Revision.ChannelName != "" {
@@ -285,6 +315,9 @@ func (s *Server) makeIndexHandler(indexer options.Indexer) ToolHandler {
 		}
 		sb.WriteString(fmt.Sprintf("Options: %d\n", result.OptionCount))
 		sb.WriteString(fmt.Sprintf("Files: %d\n", fileCount))
+		if packageCount > 0 {
+			sb.WriteString(fmt.Sprintf("Packages: %d\n", packageCount))
+		}
 		// Handle Duration which may be time.Duration or interface{}
 		if dur, ok := result.Duration.(time.Duration); ok {
 			sb.WriteString(fmt.Sprintf("Duration: %s\n", dur.Round(time.Millisecond)))
@@ -296,6 +329,85 @@ func (s *Server) makeIndexHandler(indexer options.Indexer) ToolHandler {
 	}
 }
 
+// makePackageIndexHandler creates an index_revision handler for the packages-only server.
+// It creates a revision record if needed, then indexes packages.
+func (s *Server) makePackageIndexHandler(pkgIndexer *packages.Indexer) ToolHandler {
+	return func(ctx context.Context, args map[string]interface{}) (CallToolResult, error) {
+		revision, _ := args["revision"].(string)
+		if revision == "" {
+			return ErrorContent(fmt.Errorf("revision is required")), nil
+		}
+
+		if err := packages.ValidateRevision(revision); err != nil {
+			return ErrorContent(err), nil
+		}
+
+		// Resolve channel aliases to git ref
+		ref := pkgIndexer.ResolveRevision(revision)
+
+		// Check if revision already exists
+		rev, err := s.store.GetRevision(ctx, ref)
+		if err != nil {
+			return ErrorContent(fmt.Errorf("failed to check revision: %w", err)), nil
+		}
+
+		if rev == nil {
+			// Also try by channel name
+			rev, err = s.store.GetRevisionByChannel(ctx, revision)
+			if err != nil {
+				return ErrorContent(fmt.Errorf("failed to check revision: %w", err)), nil
+			}
+		}
+
+		if rev == nil {
+			// Create a new revision record
+			commitDate, _ := pkgIndexer.GetCommitDate(ctx, ref)
+			rev = &database.Revision{
+				GitHash:     ref,
+				ChannelName: pkgIndexer.GetChannelName(revision),
+				CommitDate:  commitDate,
+			}
+			if err := s.store.CreateRevision(ctx, rev); err != nil {
+				return ErrorContent(fmt.Errorf("failed to create revision: %w", err)), nil
+			}
+		}
+
+		// Check if packages are already indexed for this revision
+		if rev.PackageCount > 0 {
+			var sb strings.Builder
+			sb.WriteString(fmt.Sprintf("Revision already indexed: %s\n", rev.GitHash))
+			if rev.ChannelName != "" {
+				sb.WriteString(fmt.Sprintf("Channel: %s\n", rev.ChannelName))
+			}
+			sb.WriteString(fmt.Sprintf("Packages: %d\n", rev.PackageCount))
+			sb.WriteString(fmt.Sprintf("Indexed at: %s\n", rev.IndexedAt.Format("2006-01-02 15:04")))
+			return CallToolResult{
+				Content: []Content{TextContent(sb.String())},
+			}, nil
+		}
+
+		// Index packages
+		pkgResult, err := pkgIndexer.IndexPackages(ctx, rev.ID, rev.GitHash)
+		if err != nil {
+			return ErrorContent(fmt.Errorf("package indexing failed: %w", err)), nil
+		}
+
+		var sb strings.Builder
+		sb.WriteString(fmt.Sprintf("Indexed revision: %s\n", rev.GitHash))
+		if rev.ChannelName != "" {
+			sb.WriteString(fmt.Sprintf("Channel: %s\n", rev.ChannelName))
+		}
+		sb.WriteString(fmt.Sprintf("Packages: %d\n", pkgResult.PackageCount))
+		if dur, ok := pkgResult.Duration.(time.Duration); ok {
+			sb.WriteString(fmt.Sprintf("Duration: %s\n", dur.Round(time.Millisecond)))
+		}
+
+		return CallToolResult{
+			Content: []Content{TextContent(sb.String())},
+		}, nil
+	}
+}
+
 // handleListRevisions handles the list_revisions tool.
 func (s *Server) handleListRevisions(ctx context.Context, args map[string]interface{}) (CallToolResult, error) {
 	revisions, err := s.store.ListRevisions(ctx)

internal/mcp/server.go

@@ -45,7 +45,7 @@ type ServerConfig struct {
 func DefaultNixOSConfig() ServerConfig {
 	return ServerConfig{
 		Name:           "nixos-options",
-		Version:        "0.3.0",
+		Version:        "0.4.0",
 		DefaultChannel: "nixos-stable",
 		SourceName:     "nixpkgs",
 		Mode:           ModeOptions,
@@ -57,7 +57,9 @@ If the current project contains a flake.lock file, you can index the exact nixpk
 
 Example: If flake.lock contains "rev": "abc123...", call index_revision with revision "abc123...".
 
-This ensures option documentation matches the nixpkgs version the project actually uses.`,
+This ensures option documentation matches the nixpkgs version the project actually uses.
+
+Note: index_revision also indexes packages when available, so both options and packages become searchable.`,
 	}
 }
 
@@ -65,7 +67,7 @@ This ensures option documentation matches the nixpkgs version the project actual
 func DefaultNixpkgsPackagesConfig() ServerConfig {
 	return ServerConfig{
 		Name:           "nixpkgs-packages",
-		Version:        "0.3.0",
+		Version:        "0.4.0",
 		DefaultChannel: "nixos-stable",
 		SourceName:     "nixpkgs",
 		Mode:           ModePackages,
@@ -73,7 +75,9 @@ func DefaultNixpkgsPackagesConfig() ServerConfig {
 
 If the current project contains a flake.lock file, you can search packages from the exact nixpkgs revision used by the project:
 1. Read the flake.lock file to find the nixpkgs "rev" field
-2. Ensure the revision is indexed (packages are indexed separately from options)
+2. Call index_revision with that git hash to index packages for that specific version
+
+Example: If flake.lock contains "rev": "abc123...", call index_revision with revision "abc123...".
 
 This ensures package information matches the nixpkgs version the project actually uses.`,
 	}
@@ -427,7 +431,7 @@ func (s *Server) getOptionToolDefinitions() []Tool {
 		},
 		{
 			Name:        "index_revision",
-			Description: fmt.Sprintf("Index a %s revision to make its options searchable", sourceRepo),
+			Description: s.indexRevisionDescription(sourceRepo),
 			InputSchema: InputSchema{
 				Type: "object",
 				Properties: map[string]Property{
@@ -464,6 +468,15 @@ func (s *Server) getOptionToolDefinitions() []Tool {
 	}
 }
 
+// indexRevisionDescription returns the description for the index_revision tool,
+// adjusted based on whether packages are also indexed.
+func (s *Server) indexRevisionDescription(sourceRepo string) string {
+	if s.config.SourceName == "nixpkgs" {
+		return fmt.Sprintf("Index a %s revision to make its options and packages searchable", sourceRepo)
+	}
+	return fmt.Sprintf("Index a %s revision to make its options searchable", sourceRepo)
+}
+
 // getPackageToolDefinitions returns the tool definitions for packages mode.
 func (s *Server) getPackageToolDefinitions() []Tool {
 	exampleChannels := "'nixos-unstable', 'nixos-24.05'"
@@ -547,6 +560,20 @@ func (s *Server) getPackageToolDefinitions() []Tool {
 				Required: []string{"path"},
 			},
 		},
+		{
+			Name:        "index_revision",
+			Description: "Index a nixpkgs revision to make its packages searchable",
+			InputSchema: InputSchema{
+				Type: "object",
+				Properties: map[string]Property{
+					"revision": {
+						Type:        "string",
+						Description: fmt.Sprintf("Git hash (full or short) or channel name (e.g., %s)", exampleChannels),
+					},
+				},
+				Required: []string{"revision"},
+			},
+		},
 		{
 			Name:        "list_revisions",
 			Description: "List all indexed nixpkgs revisions",

internal/mcp/server_test.go

@@ -10,6 +10,7 @@ import (
 
 	"git.t-juice.club/torjus/labmcp/internal/database"
 	"git.t-juice.club/torjus/labmcp/internal/nixos"
+	"git.t-juice.club/torjus/labmcp/internal/packages"
 )
 
 func TestServerInitialize(t *testing.T) {
@@ -145,6 +146,110 @@ func TestServerNotification(t *testing.T) {
 	}
 }
 
+func TestPackagesServerToolsList(t *testing.T) {
+	store := setupTestStore(t)
+	server := NewServer(store, nil, DefaultNixpkgsPackagesConfig())
+
+	pkgIndexer := packages.NewIndexer(store)
+	server.RegisterPackageHandlers(pkgIndexer)
+
+	input := `{"jsonrpc":"2.0","id":1,"method":"tools/list"}`
+
+	resp := runRequest(t, server, input)
+
+	if resp.Error != nil {
+		t.Fatalf("Unexpected error: %v", resp.Error)
+	}
+
+	result, ok := resp.Result.(map[string]interface{})
+	if !ok {
+		t.Fatalf("Expected map result, got %T", resp.Result)
+	}
+
+	tools, ok := result["tools"].([]interface{})
+	if !ok {
+		t.Fatalf("Expected tools array, got %T", result["tools"])
+	}
+
+	// Should have 6 tools (search_packages, get_package, get_file, index_revision, list_revisions, delete_revision)
+	if len(tools) != 6 {
+		t.Errorf("Expected 6 tools, got %d", len(tools))
+	}
+
+	expectedTools := map[string]bool{
+		"search_packages": false,
+		"get_package":     false,
+		"get_file":        false,
+		"index_revision":  false,
+		"list_revisions":  false,
+		"delete_revision": false,
+	}
+
+	for _, tool := range tools {
+		toolMap := tool.(map[string]interface{})
+		name := toolMap["name"].(string)
+		if _, ok := expectedTools[name]; ok {
+			expectedTools[name] = true
+		}
+	}
+
+	for name, found := range expectedTools {
+		if !found {
+			t.Errorf("Tool %q not found in tools list", name)
+		}
+	}
+}
+
+func TestOptionsServerWithPackagesToolsList(t *testing.T) {
+	store := setupTestStore(t)
+	server := NewServer(store, nil, DefaultNixOSConfig())
+
+	indexer := nixos.NewIndexer(store)
+	pkgIndexer := packages.NewIndexer(store)
+	server.RegisterHandlersWithPackages(indexer, pkgIndexer)
+
+	input := `{"jsonrpc":"2.0","id":1,"method":"tools/list"}`
+
+	resp := runRequest(t, server, input)
+
+	if resp.Error != nil {
+		t.Fatalf("Unexpected error: %v", resp.Error)
+	}
+
+	result, ok := resp.Result.(map[string]interface{})
+	if !ok {
+		t.Fatalf("Expected map result, got %T", resp.Result)
+	}
+
+	tools, ok := result["tools"].([]interface{})
+	if !ok {
+		t.Fatalf("Expected tools array, got %T", result["tools"])
+	}
+
+	// Should still have 6 tools (same as options-only)
+	if len(tools) != 6 {
+		t.Errorf("Expected 6 tools, got %d", len(tools))
+	}
+
+	// Verify index_revision is present
+	found := false
+	for _, tool := range tools {
+		toolMap := tool.(map[string]interface{})
+		if toolMap["name"].(string) == "index_revision" {
+			found = true
+			// For nixpkgs source, description should mention packages
+			desc := toolMap["description"].(string)
+			if !strings.Contains(desc, "packages") {
+				t.Errorf("index_revision description should mention packages, got: %s", desc)
+			}
+			break
+		}
+	}
+	if !found {
+		t.Error("index_revision tool not found in tools list")
+	}
+}
+
 func TestGetFilePathValidation(t *testing.T) {
 	store := setupTestStore(t)
 	server := setupTestServer(t, store)

nix/package.nix

@@ -7,7 +7,7 @@
 
 buildGoModule {
   inherit pname src;
-  version = "0.3.0";
+  version = "0.4.0";
 
   vendorHash = "sha256-XrTtiaQT5br+0ZXz8//rc04GZn/HlQk7l8Nx/+Uil/I=";