Question

So the following program should take in an input and output file as command line arguments.

class FileCopy
{
public static void main(String[] args) throws IOException
{
    String infile = null;
    String outfile = null;
    BufferedReader stdin = new BufferedReader(new InputStreamReader(System.in));    

    if (args.length >= 2) //both files given via command line
    {
        infile = args[0];
        if (fileExists(infile) == false)
        {
            infile = getInputFile();
        }
        outfile = args[1];
    }
    else if (args.length == 1) //input file given via command line
    {
        infile = args[0];
        outfile = getOutputFile(infile);
    }
    else //no files given on command line
    {
        infile = getInputFile();
        outfile = getOutputFile(infile);
    }

    //create file objects to use
    File in = new File(infile);
    File out = new File(outfile);

    /*
     *rest of code
     */
}

//get the input file from the user if given file does not exist
public static String getInputFile() //throws IOException
{
    BufferedReader stdin = new BufferedReader(new InputStreamReader(System.in));
    String fileName = null;
    boolean haveFile = false;

    while(haveFile == false)
    {
        System.out.println("Enter a valid filename for input:");
        System.out.print(">> ");
        try
        {
            fileName = stdin.readLine();
        }
        catch (IOException e)
        {
            System.out.println("Caught exception: " + e);
        }
        haveFile = fileExists(fileName);
    }

    return fileName;    
}

//get the output file and test things
public static String getOutputFile(String infile)
{
    BufferedReader stdin = new BufferedReader(new InputStreamReader(System.in));
    File input = new File(infile);
    String filename = null;
    boolean more = true;
    while(more)
    {
        System.out.println("Enter a valid filename for output:");
        System.out.print(">> ");
        try
        {
            filename = stdin.readLine();
        }
        catch (IOException e)
        {
            System.out.println("Caught exception: " + e);
        }
        File output = new File(filename);
        if (output.exists())
        {
            more = false;
        }
        if (filename == infile)
        {
            int selection;
            String inputString = null;

            System.out.println("The output file given matches the input file. Please choose an option:");
            System.out.println("1) Enter new filename");
            System.out.println("2) Overwrite existing file");
            System.out.println("3) Backup existing file");
            System.out.print(">> ");
            try
            {
                inputString = stdin.readLine();
            }
            catch (IOException e)
            {
                System.out.println("Caught exception: " + e);
            }
            selection = Integer.valueOf(inputString);
            switch (selection)
            {
                case 1: //new filename
                case 2: //overwrite
                case 3: //backup
                default: System.exit(0);
            }
        }
    }
    return null;
}

//check the given file to see if it exists in the current working directory
public static boolean fileExists(String n)
{
    return (new File(n)).exists();
}
}

Answer 1

One detail that I believe you have missed:

When your program has only one argument (args.length == 1), i.e. when only the input file is defined, fileExists() is not called at all; infile is set to args[0] with no validation at all. You should probably add a specific check as you have done for the two-argument case.