Implemented the file identifier functionality for Java.

Also fixed flatc not outputting these identifiers for files
compiled on the command-line.

Bug: 16983987
Change-Id: I8b714cfea3a8e144fa52133f62b2f7eda6eb044a
Tested: on Linux

docs/html/md__cpp_usage.html

@@ -104,6 +104,7 @@ assert(inv->Get(9) == 9);
 <p>if <code>ok</code> is true, the buffer is safe to read.</p>
 <p>Besides untrusted data, this function may be useful to call in debug mode, as extra insurance against data being corrupted somewhere along the way.</p>
 <p>While verifying a buffer isn't "free", it is typically faster than a full traversal (since any scalar data is not actually touched), and since it may cause the buffer to be brought into cache before reading, the actual overhead may be even lower than expected.</p>
+<p>In specialized cases where a denial of service attack is possible, the verifier has two additional constructor arguments that allow you to limit the nesting depth and total amount of tables the verifier may encounter before declaring the buffer malformed.</p>
 <h2>Text &amp; schema parsing</h2>
 <p>Using binary buffers with the generated header provides a super low overhead use of FlatBuffer data. There are, however, times when you want to use text formats, for example because it interacts better with source control, or you want to give your users easy access to data.</p>
 <p>Another reason might be that you already have a lot of data in JSON format, or a tool that generates JSON, and if you can write a schema for it, this will provide you an easy way to use that data directly.</p>