@Adi Tiwari, I've found the cause. Runtime.getRuntime.exec() doesn't execute a shell command directly, it executes an executable with arguments. "echo" is a builtin shell command. It is actually a part of the argument of the executable sh with the option -c. Commands like ls are actual executables. You can use type echo and type ls command in adb shell to see the difference.
So final code is:

String[] cmdline = { "sh", "-c", "echo $BOOTCLASSPATH" }; 
Runtime.getRuntime().exec(cmdline);

The first thing you should do is to log the stderr stream that is available for your process as well. This will give you information about what is wrong with your command.

Your command is not correctly processed as it is seen as one command. The reason is explained in this answer.

The solution is to use a String[] as an argument of exec and explicitly execute the command with the shell. I wrote some code that executes your command, but it is in Java on an unrooted device. Still, it generates output and grep works.

String[] arrayCommand = {"sh", "-c","dumpsys telephony.registry | grep \"permission\""};
            
Runtime r = Runtime.getRuntime();
Process process = r.exec(arrayCommand);

String stdoutString = convertInputStreamToString(process.getInputStream());
String stderrString = convertInputStreamToString(process.getErrorStream());

If you are using service to check every 5 seconds then you must return START_NOT_STICKY from override method onStartCommand() if you want to prevent it start service automatically when it crashes.

Finally after weeks of searching:

Runtime.getRuntime().exec(new String[]{"/system/bin/su","-c","reboot now"});

You probably still need to have the WRITE_EXTERNAL_STORAGE permission, in case you do not have that.

Your bigger problem is that cp is not in any sort of PATH. In fact, I do not see the cp command anywhere on the Android 2.2 emulator, though I have not done an exhaustive search.

The way a savvy programmer would solve this is using Java, since that eliminates your dependency on undocumented/unsupported command-line binaries.

First, you should wrap calls to exec in a try-catch-clause to catch IOExceptions.

Second, use exec(java.lang.String[]) to execute a command with parameters. For example, similar to

Runtime.getRuntime().exec(new String[]{ "shell", "/system/bin/chmod", "0777", sdCard.getAbsolutePath() + "/" + nativeFile });

That's most likely the bug fixed in this Github commit. In essence, it deadlocks directly after fork() but before doing the actual exec() because somebody tried to malloc.

You can execute ls with provided path for which folders should be listed

Runtime.getRuntime().exec(new String[] { "ls", "\\tmp"});

Redirection (>) is not the OS feature. This is a feature of shell. To make it working from java you have to run something like the following:

/bin/sh yourcommand > yourfile

i.e. in your case:

/bin/sh cat /sdcard/file1.mpg /sdcard/file2.mpg > /sdcard/out.mpg

BUT could you please explain me why are you doeing this? Do you understand that this command is exact equivalent of cp /sdcard/file1.mpg /sdcard/file2.mpg /sdcard/out.mpg that can be coded in pure java without running any command line? Unless you have special reasons go on it! Write pure java code when it is possible. It is easier to debug, support and maintain.

The method Runtime.exec(String prog, String[] envp, File directory) requires you to give environment in the form name=value in the String[] envp.

But you are using it to pass arguments to your php program.

Use the following method instead,

Process exec (String[] progArray, String[] envp, File directory);

and pass all your command line arguments too in the first array itself.

Your command should look like:

String[] progArray= {"./php", "-f", getFilesDir().getAbsolutePath()+"/phprun.php"}; // ">>","phpoutput.txt"
File dir=  new File(getFilesDir().getAbsolutePath());
Process p = Runtime.getRuntime().exec(progArray,null,dir);