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There are quite some things you can improve here, this list may not cover everything that could be improved though:


Adhere to the Java naming conventions. Classes are named in PascalCase for example, so it would be public class Meow. On other places it seems fine.
Use proper indentation everywhere, this definately applies to the main method inside public class meow, as all items should be intended one to the right. This may also apply to the while loops, I would prefer to write while(sc1.hasNext()){ as while (sc1.hasNext()) { for readability.
Variable names are not expensive. sc1, sc2 are dubious, but could be ok. However inW and inL are plain alarming, the fact that you need to comment to explain them is a bad sign. My suggestions are wordIndex and lineIndex.
Consider using a StringBuilder over dealing with raw strings. This means for example that:

String text = "", code = "";
while(sc1.hasNext()){
     text += sc1.next() + " ";
}


could be rewritten as:

StringBuilder sb = new StringBuilder();
while (sc1.hasNext()) {
        sb.append(sc1.next()).append(' ');
}
String text = sb.toString();

You have a bug in your second while-loop. You check for sc2.hasNext() and you take two times sc2.nextInt(). Your hasX() and nextX() calls should always match. This means that in the loop per iteration in total there should be two hasNextInt() calls with two nextInt() calls.
The same deal about StringBuilder applies here to your second while-loop for building code.
In the future you can consider switching to using the java.nio.Path API, over the old java.io.File API. I will not show more code here on how to do it, as it would completely change the structure of the program and is best used in conjunction with Java 8, which is not in the scope of this answer.