You don't need to include spaces. The ProcessBuilder will deal with that for you. Just pass in your arguments one by one, without space:

ProcessBuilder pb = new ProcessBuilder(
    dir + "library/crc",
    "-s",
    fileName,
    addressRanges);

You are executing this command: java directory second 5

That is not a valid invocation of the java command. The syntax is:

java [-options] class [args...]

Passing a class name is correct. Passing a directory is not correct.

You can see the syntax for yourself by running java -h, or by reading the documentation. No need to guess what is allowed.

What you are allowed to do is pass a directory as an argument to the -cp option, which is probably what you intended:

new ProcessBuilder("java", "-cp", curDir, "second", "5");

Be aware that class names are case sensitive. If your class is named Second, you must pass the same name, with a capital S, to your java command:

new ProcessBuilder("java", "-cp", curDir, "Second", "5");
                                           ↑
                                           Uppercase S

All file paths are either absolute paths, or are implicitly relative to the current directory. You don’t need all those lines dealing with currentRelativePath. Just write this:

String curDir = "src";