diff --git a/.gitignore b/.gitignore
index 7192c4b..86cf3ce 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,6 +9,7 @@
 /arxiv-processor/arxiv-processor
 /json2md/json2md
 /llm_processor/llm_processor
+paper-system
 
 # Dependency directories
 vendor/
@@ -27,6 +28,8 @@ temp_*.json
 .env
 
 # Generated output files
+*.md
+*.json
 papers.json
 newpapers.md.gz
 arxiv-processor/newpapers.json
diff --git a/main.go b/main.go
index 7d93820..3963fb8 100644
--- a/main.go
+++ b/main.go
@@ -169,10 +169,11 @@ func main() {
 		if err != nil {
 			log.Fatalf("Failed to marshal papers: %v", err)
 		}
-		if err := os.WriteFile("papers.json", papersJSON, 0644); err != nil {
+		jsonName := fmt.Sprintf("%s-%s-%s-papers.json", *start, *end, *search)
+		if err := os.WriteFile(jsonName, papersJSON, 0644); err != nil {
 			log.Fatalf("Failed to save papers JSON: %v", err)
 		}
-		log.Printf("Successfully saved papers to papers.json")
+		log.Printf("Successfully saved papers to %s", jsonName)
 	}
 
 	// Print paper titles for verification
@@ -182,12 +183,17 @@ func main() {
 	}
 
 	// Save papers to temporary file for LLM processing
-	tempInput := "temp_input.json"
+	tempInput, err := os.CreateTemp("", "arxiv-process-*.tmp")
+	if err != nil {
+		log.Fatalf("Failed to create temp file: %v", err)
+	}
+	defer os.Remove(tempInput.Name())
+
 	tempJSON, err := json.Marshal(llmPapers)
 	if err != nil {
 		log.Fatalf("Failed to marshal papers for LLM: %v", err)
 	}
-	if err := os.WriteFile(tempInput, tempJSON, 0644); err != nil {
+	if err := os.WriteFile(tempInput.Name(), tempJSON, 0644); err != nil {
 		log.Fatalf("Failed to save temp input JSON: %v", err)
 	}
 
@@ -201,30 +207,38 @@ func main() {
 	llmProcessor := processor.NewProcessor(*model, 32, apiKey) // 32 = batch size from README
 	log.Printf("Initialized LLM processor with model %s", *model)
 
-	tempOutput := "temp_output.json"
+	tempOutput, err := os.CreateTemp("", "arxiv-process-*.tmp")
+	if err != nil {
+		log.Fatalf("Failed to create temp file: %v", err)
+	}
+	defer os.Remove(tempOutput.Name())
+
 	log.Printf("Processing papers with criteria from %s", *criteriaFile)
-	if err := llmProcessor.ProcessPapers(ctx, tempInput, tempOutput, *criteriaFile, 1*time.Second); err != nil {
+	if err := llmProcessor.ProcessPapers(ctx, tempInput.Name(), tempOutput.Name(), *criteriaFile, 1*time.Second); err != nil {
 		log.Fatalf("LLM processing failed: %v", err)
 	}
 	log.Printf("LLM processing complete, results saved to %s", tempOutput)
 
 	// Generate markdown
 	log.Printf("Generating markdown output")
-	decisions, err := lib.ProcessJSONFile(tempOutput)
+	decisions, err := lib.ProcessJSONFile(tempOutput.Name())
 	if err != nil {
 		log.Fatalf("Failed to process JSON: %v", err)
 	}
 	log.Printf("Processed decisions: %d accepted, %d rejected", len(decisions.Accepted), len(decisions.Rejected))
 
+	defaultOutput := fmt.Sprintf("%s-%s-%s-papers.md", *start, *end, *search)
+	if *output == "papers.md" && usingArxiv {
+		*output = defaultOutput
+	}
+
 	if err := lib.GenerateMarkdown(decisions, *output); err != nil {
 		log.Fatalf("Markdown generation failed: %v", err)
 	}
 	log.Printf("Generated markdown output at %s", *output)
 
-	// Cleanup temp files
-	os.Remove(tempInput)
-	os.Remove(tempOutput)
-	log.Printf("Cleaned up temporary files")
+	// Temp files cleaned up by defer statements
+	log.Printf("Cleanup complete")
 
 	log.Printf("Process complete. Results saved to %s", *output)
 }
diff --git a/paper-system b/paper-system
deleted file mode 100755
index 078a66c..0000000
Binary files a/paper-system and /dev/null differ