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how can we simulate Ctrl+C to stop the console app from waiting for user input in java

I am trying to test a command line app that waits for the user input after every step. I am able to test the app using System Rules provided by Stefan Birkner. Currently, I provide inputs from the beginning to the end which works like a charm and I can assert the final output from system log.
However, I want to test for the negative cases before the end of the app for which I give invalid inputs in the beginning to evaluate the error message. When invalid inputs are given, the console prints an error message and keeps waiting for the user to provide a valid input. How do I send Ctrl+C using as shown below:
systemInMock.provideLines(Ctrl+C);
systemInMock.provideLines accepts only strings. Is there a way to send Ctrl+C signal?
An example of my junit test is shown below:
#Test
public void testInValidMarker() throws Exception{
systemInMock.provideLines("abc","def","1");
Main.main(new String[]{});
assertTrue(systemOutRule.getLog().contains("Invalid marker, try again"));
}
Appreciate your help!

If I'm not mistaken, when you do ctrl+c, it doesn't actually get written to console. If that's true, then in no case will your program ever be given ctrl+c, so provideLines will never be in a position where it is given ctrl+c.
For proof, open up cmd and type in a program with program arguments (in my case, I use ant). If you type ant and then ctrl+c, the cursor is moved to a new line.
There are two ways you can control termination behavior:
You can use a shutdown hook (found from this previously asked question ). Doing this will allow you to handle what happens (potentially with issues).
Or you could create your own termination argument like -q or q, which would trigger an action to end the program (maybe a System.exit(1)). This way you can mock that input.

In UNIX/Linux, when you type CTRL-C, your shell intercepts it and sends the process a SIGINT signal -- see: How does Ctrl-C terminate a child process?
Therefore the System Rules project doesn't have anything to help you -- in this situation the process doesn't receive any character input.
By default, the whole JVM shuts down when it receives SIGINT. This is obviously bad news for a running test.
The SO question Signal handling using "TERM" -- may be of use.
A side effect of Java's portability is that for some OS features, it either abstracts things away until they're unrecognisable, or doesn't expose them at all.
I suspect what you're asking for can't be achieved.
If you're allowed to change the requirements slightly, you could ask the user to close with CTRL-D -- this closes stdin with EOF.
Although it's quite the overkill, you could launch a whole new JVM running your program, using ProcessBuilder. You might imagine you'd get an API to send arbitrary signals to that process. But for portability reasons, all you can do is process.destroy(), which sends SIGTERM.

Tried this as a comment, but it didn't read right. It's not exactly an "Answer" though.
So Java is really bad at console input. It reads an entire line at once and you can't do anything about it--there is no way to trap special characters or even see any of the input before the user hits return. Also I think a ctrl-d will close your input session--(Add that test to your use case if you don't use any other suggestion here because it can put you into a state you didn't expect!)
Three suggestions:
The simplest: If you can use a GUI and aren't really looking for an ongoing input/response REPL the simplest answer is usually to use JOptionPane to throw up a quick dialog. It's a one-line solution to get some user input, but not so good for an ongoing command-driven system.
If you can't use swing (If you are running headless) then you may have little choice, but you can use the JLine library. That will give you a lot more flexibility. This is how Groovysh does it's REPL. It will let you see each character as it is typed and do things like completion where a user might type part of a file name and hit tab and you put the rest in for him.
If you don't want to use JLine but want a REPL feel there is also a more complex GUI solution--create a swing console window. A trivial solution would just be a text input box to allow typing and a text area to display results, but there are certainly libraries out there with more complete console solutions.
The point here is that using Java standard input alone is just not a good solution for anything beyond a trivial/personal script--and even then I avoid it. Perhaps not the answer you asked for, but maybe it's the one you need :)

Writing Java interpreter Plugin

A few days back I wrote a Textinterpreter plugin in Eclipse which basically takes a text file and simply printout it's content in the console. It does this by first taking a text file and converts it to a string.
then it makes an Arraylist out of it from which each line is printed out in the console.
List<String> mLines = new LinkedList<String>(Arrays.asList(string)
while(!mLines.isEmpty())) {
String line = mLines.remove(0);
if(line.equals("Stop...")){
debug(DebugAction.Suspend);
}
System.out.println(">>> " + line + " <<<");
}
You can see an if statement in code above which checks whether "Stop..." is written on any line in the text file and if it is then the debug() funtion is called(which suspends running unless the user press resume() button in debugmode.)
Now I want to do the same for .java files. i.e write a Java interpreter plugin which execute a java file normally until it finds "Stop..." written in code.
Any Suggestions?

I don't think you really want to implement a Java interpreter, that'd be a huge project keeping you busy for some years maybe.
The most natural solution for you task might be to scan the Java source file and automatically create breakpoints at each Stop statement. Then run the application in debug mode and you get the desired behaviour. Since you only need the line number for creating the breakpoint you can actually keep reading/scanning files line-by-line.
To get additional statements executed (like calling debug(..)) add your snippet as a breakpoint condition (followed by return true; to tell the debug to stop indeed).

Java CLI App - keep input from scrolling up

I get that this isn't possible to do with normal java, although if there are any libraries out this it would be very useful.
Essentially, I'm designing a console app and running into an issue that when output happens while something is typed in the input line, that input text will move up and appear before the line that just got output. Is it possible to fix this in some form so that the text you are inputting that stays at the bottom?
EX:
I'm typing something as input into my commandline app, and then the program prints something WHILE I'm typing - this causes what was originally on the input line to be scrolled up with whatever the output text was. When you are trying to type something in this can obviously be detrimental. I know it's possible to prevent this.. (Other programs have done it... EX: Minecraft Server)
(If I need to be more descriptive I can.)

You could use the help of threads. One that listens to user input, the other process the actual output. This problem is similar to basic race condition problems when multiple threads attempt to read and write to a shared resource.
Your shared resource is that console. You need to keep the Input/Output operations synchronized. Have a look at race condition.

Want to get standard output or error when using Process

I want to use "which hoge" for obtaining a path for the hoge in Java code.
when "hoge" exists, the path can be obtained by Process#getInputStream.
but when "hoge" doesn't exist, both input stream and error stream from Process#get(Input|Error)Streams give "null".
but in terminal (OS X), if I try "which unexists", I get "unexists not found".
where does the message "unexists not found" go? How can I get this?
Does Java use another "which"?

Your shell probably has "which" as a built-in command, so it doesn't use the /bin/which program. There are likely many differences between the two. You can check which which you use with the command "type which" and use the program instead of the built-in command using /bin/which.
From Java, you can know if a result was found by checking the process exit status returned by Process.waitFor(). If the status is 0 which found a match, if non-zero it didn't or there was some other error.

What determines where a System.out.println(args) command prints to?

It may be a silly question but I can't find anything on the web with the answer. What (if anything) determines where the args of a System.out.println(args) command will be displayed? I've been using an IO class created by my lecturer which created it's own GUI and wrote to specific areas of that by default but now that I am making my own programs I am struggling to get the text/images/whatever to display where I want it to.

From the Javadocs for System.out:
The "standard" output stream. This stream is already open and ready to accept output data. Typically this stream corresponds to display output or another output destination specified by the host environment or user.
In most computing environments, there are three standard streams associated with a process.
Note, however, that System.out can be reassigned in Java, by using System.setOut().

Depending on the operating system you're using, each process has associated a standard input, standard output and a standard error. If you execute your program in a console, the it will be your standard input, output and error.
For instance, in Linux you can redirect the standard output with redirection operators like this:
java MyClass > fileAsOutput.txt