Any way to run shell commands on android programmatically?

Okay this is what exactly worked for me just in case anyone needs it in the future... :)

Surround in try and catch

try {
    Process process = Runtime.getRuntime().exec("top -n 1 -d 1");
    BufferedReader in = new BufferedReader(new InputStreamReader(process.getInputStream()));
} catch (InterruptedException e) {
    e.printStackTrace();
}

Check out Log Collector as an example. Here is the relevant file.

The key is here:

ArrayList<String> commandLine = new ArrayList<String>();
commandLine.add("logcat");//$NON-NLS-1$
[...]

Process process = Runtime.getRuntime().exec(commandLine);
BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(process.getInputStream()));