I am in the process of switching from Eclipse to IntelliJ. I have included a file "input.txt" in my project, but I am getting a FileNotFoundException when I write Java code to access it. What am I doing wrong?

It's not the issue, that the file could not be found in IntelliJ. It's the fact, that your compiler says, that the file could possible not found at runtime. So you have to handle the FileNotFoundException with a try-catch block around like this:
try { BufferedReader reader = new BufferedReader(new FileReader("./input.txt")); // read the file // ... } catch (FileNotFoundException e) { // do something, when the file could not be found on the system System.out.println("The file doesn't exist."); } catch (IOException e) { // do something, when the file is not readable System.out.println("The file could not be read."); } catch (/* other exceptions... */) { // do something else on some other exception // ... } Of course, you already know, that the file will be found, but not the compiler!
Basically read about Exceptions: http://docs.oracle.com/javase/tutorial/essential/exceptions/
You can also throw the FileNotFoundException into your main method, your output just won't be as pretty.
public static void main(String[] args) throws FileNotFoundException {