test: improve file indexing benchmarks

- BenchmarkIndexRevisionWithFiles now reports separate timing for
  options indexing (options_ms) and file indexing (files_ms)
- Add BenchmarkIndexFilesOnly to measure file indexing in isolation

Run with:
  go test -bench=BenchmarkIndexFilesOnly -benchtime=1x -timeout=60m ./internal/nixos/...

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

internal/nixos/indexer_test.go

@@ -4,6 +4,7 @@ import (
 	"context"
 	"os/exec"
 	"testing"
+	"time"
 
 	"git.t-juice.club/torjus/labmcp/internal/database"
 )
@@ -86,12 +87,55 @@ func BenchmarkIndexRevisionWithFiles(b *testing.B) {
 			b.Fatalf("IndexRevision failed: %v", err)
 		}
 
+		fileStart := time.Now()
+		fileCount, err := indexer.IndexFiles(ctx, result.Revision.ID, TestNixpkgsRevision)
+		if err != nil {
+			b.Fatalf("IndexFiles failed: %v", err)
+		}
+		fileDuration := time.Since(fileStart)
+
+		b.ReportMetric(float64(result.OptionCount), "options")
+		b.ReportMetric(float64(result.Duration.Milliseconds()), "options_ms")
+		b.ReportMetric(float64(fileCount), "files")
+		b.ReportMetric(float64(fileDuration.Milliseconds()), "files_ms")
+	}
+}
+
+// BenchmarkIndexFilesOnly benchmarks only the file indexing phase.
+// Assumes options are already indexed. Useful for measuring file indexing in isolation.
+// Run with: go test -bench=BenchmarkIndexFilesOnly -benchtime=1x -timeout=60m ./internal/nixos/...
+func BenchmarkIndexFilesOnly(b *testing.B) {
+	if _, err := exec.LookPath("nix-build"); err != nil {
+		b.Skip("nix-build not found, skipping indexer benchmark")
+	}
+
+	store, err := database.NewSQLiteStore(":memory:")
+	if err != nil {
+		b.Fatalf("Failed to create store: %v", err)
+	}
+	defer store.Close()
+
+	ctx := context.Background()
+	if err := store.Initialize(ctx); err != nil {
+		b.Fatalf("Failed to initialize store: %v", err)
+	}
+
+	indexer := NewIndexer(store)
+
+	// Index options first (outside of benchmark timing)
+	result, err := indexer.IndexRevision(ctx, TestNixpkgsRevision)
+	if err != nil {
+		b.Fatalf("IndexRevision failed: %v", err)
+	}
+	b.Logf("Pre-indexed %d options", result.OptionCount)
+
+	b.ResetTimer()
+	for i := 0; i < b.N; i++ {
 		fileCount, err := indexer.IndexFiles(ctx, result.Revision.ID, TestNixpkgsRevision)
 		if err != nil {
 			b.Fatalf("IndexFiles failed: %v", err)
 		}
 
-		b.ReportMetric(float64(result.OptionCount), "options")
 		b.ReportMetric(float64(fileCount), "files")
 	}
 }