Code review comment: What would happen if theres already a Ballerina.toml file ?

Code under review:
public void execute() {
        PrintStream out = System.out;

        
        Path projectPath = Paths.get(System.getProperty(USER_DIR));
        Scanner scanner = new Scanner(System.in, Charset.defaultCharset().name());
        try {
            Manifest manifest = null;

            if (helpFlag) {
                String commandUsageInfo = BLauncherCmd.getCommandUsageInfo(parentCmdParser, "init");
                outStream.println(commandUsageInfo);
                return;
            }

            List<SrcFile> sourceFiles = new ArrayList<>();
            List<PackageMdFile> packageMdFiles = new ArrayList<>();
            if (interactiveFlag) {

                
                out.print("Create Ballerina.toml [yes/y, no/n]: (y) ");
                String createToml = scanner.nextLine().trim();

                if (createToml.equalsIgnoreCase("yes") || createToml.equalsIgnoreCase("y") ||
                        createToml.isEmpty()) {
                    manifest = new Manifest();

                    String defaultOrg = guessOrgName();

                    
                    out.print("Organization name: (" + defaultOrg + ") ");
                    String orgName = scanner.nextLine().trim();
                    manifest.setName(orgName.isEmpty() ? defaultOrg : orgName);

                    String version;
                    do {
                        out.print("Version: (" + DEFAULT_VERSION + ") ");
                        version = scanner.nextLine().trim();
                        version = version.isEmpty() ? DEFAULT_VERSION : version;
                    } while (!validateVersion(out, version));

                    manifest.setVersion(version);
                }

                String srcInput;
                boolean validInput = false;
                do {
                    out.print("Ballerina source [service/s, main/m, finish/f]: (f) ");
                    srcInput = scanner.nextLine().trim();

                    if (srcInput.equalsIgnoreCase("service") || srcInput.equalsIgnoreCase("s") ||
                            srcInput.isEmpty()) {
                        out.print("Package for the service : (no package) ");
                        String packageName = scanner.nextLine().trim();
                        SrcFile srcFile = new SrcFile(packageName, FileType.SERVICE);
                        sourceFiles.add(srcFile);
                        if (!packageName.isEmpty()) {
                            PackageMdFile packageMdFile = new PackageMdFile(packageName, FileType.SERVICE);
                            packageMdFiles.add(packageMdFile);
                        }
                    } else if (srcInput.equalsIgnoreCase("main") || srcInput.equalsIgnoreCase("m")) {
                        out.print("Package for the main : (no package) ");
                        String packageName = scanner.nextLine().trim();
                        SrcFile srcFile = new SrcFile(packageName, FileType.MAIN);
                        sourceFiles.add(srcFile);
                        if (!packageName.isEmpty()) {
                            PackageMdFile packageMdFile = new PackageMdFile(packageName, FileType.MAIN);
                            packageMdFiles.add(packageMdFile);
                        }
                    } else if (srcInput.isEmpty() || srcInput.equalsIgnoreCase("f")) {
                        validInput = true;
                    } else {
                        out.println("Invalid input");
                    }
                } while (!validInput);

                out.print("\n");
            } else {
                manifest = new Manifest();
                manifest.setName(guessOrgName());
                manifest.setVersion(DEFAULT_VERSION);
                if (isDirEmpty(projectPath)) {
                    SrcFile srcFile = new SrcFile("", FileType.SERVICE);
                    sourceFiles.add(srcFile);
                }
            }

            InitHandler.initialize(projectPath, manifest, sourceFiles, packageMdFiles);
            out.println("Ballerina project initialized");

        } catch (IOException e) {
            out.println("Error occurred while creating project: " + e.getMessage());
        }
    }

Line commented on: manifest.setVersion(DEFAULT_VERSION);

Revised code:
public void execute() {
        PrintStream out = System.out;

        
        Path projectPath = Paths.get(System.getProperty(USER_DIR));
        Scanner scanner = new Scanner(System.in, Charset.defaultCharset().name());
        try {
            Manifest manifest = null;

            if (helpFlag) {
                String commandUsageInfo = BLauncherCmd.getCommandUsageInfo(parentCmdParser, "init");
                outStream.println(commandUsageInfo);
                return;
            }

            List<SrcFile> sourceFiles = new ArrayList<>();
            List<PackageMdFile> packageMdFiles = new ArrayList<>();
            if (interactiveFlag) {

                
                out.print("Create Ballerina.toml [yes/y, no/n]: (y) ");
                String createToml = scanner.nextLine().trim();

                if (createToml.equalsIgnoreCase("yes") || createToml.equalsIgnoreCase("y") || createToml.isEmpty()) {
                    manifest = new Manifest();

                    String defaultOrg = guessOrgName();

                    
                    out.print("Organization name: (" + defaultOrg + ") ");
                    String orgName = scanner.nextLine().trim();
                    manifest.setName(orgName.isEmpty() ? defaultOrg : orgName);

                    String version;
                    do {
                        out.print("Version: (" + DEFAULT_VERSION + ") ");
                        version = scanner.nextLine().trim();
                        version = version.isEmpty() ? DEFAULT_VERSION : version;
                    } while (!validateVersion(out, version));

                    manifest.setVersion(version);
                }

                String srcInput;
                boolean validInput = false;
                do {
                    out.print("Ballerina source [service/s, main/m, finish/f]: (f) ");
                    srcInput = scanner.nextLine().trim();

                    if (srcInput.equalsIgnoreCase("service") || srcInput.equalsIgnoreCase("s") || srcInput.isEmpty()) {
                        out.print("Package for the service : (no package) ");
                        String packageName = scanner.nextLine().trim();
                        SrcFile srcFile = new SrcFile(packageName, FileType.SERVICE);
                        sourceFiles.add(srcFile);
                        if (!packageName.isEmpty()) {
                            PackageMdFile packageMdFile = new PackageMdFile(packageName, FileType.SERVICE);
                            packageMdFiles.add(packageMdFile);
                        }
                    } else if (srcInput.equalsIgnoreCase("main") || srcInput.equalsIgnoreCase("m")) {
                        out.print("Package for the main : (no package) ");
                        String packageName = scanner.nextLine().trim();
                        SrcFile srcFile = new SrcFile(packageName, FileType.MAIN);
                        sourceFiles.add(srcFile);
                        if (!packageName.isEmpty()) {
                            PackageMdFile packageMdFile = new PackageMdFile(packageName, FileType.MAIN);
                            packageMdFiles.add(packageMdFile);
                        }
                    } else if (srcInput.isEmpty() || srcInput.equalsIgnoreCase("f")) {
                        validInput = true;
                    } else {
                        out.println("Invalid input");
                    }
                } while (!validInput);

                out.print("\n");
            } else {
                manifest = new Manifest();
                manifest.setName(guessOrgName());
                manifest.setVersion(DEFAULT_VERSION);
                if (isDirEmpty(projectPath)) {
                    SrcFile srcFile = new SrcFile("", FileType.SERVICE);
                    sourceFiles.add(srcFile);
                }
            }

            InitHandler.initialize(projectPath, manifest, sourceFiles, packageMdFiles);
            out.println("Ballerina project initialized");

        } catch (IOException e) {
            out.println("Error occurred while creating project: " + e.getMessage());
        }
    }