How do I read the manifest file for a webapp running in apache tomcat?

Maybe your side-effects come from the fact that almost all jars include a MANIFEST.MF and you're not getting the right one. To read the MANIFEST.MF from the webapp, I would say:

ServletContext application = getServletConfig().getServletContext();
InputStream inputStream = application.getResourceAsStream("/META-INF/MANIFEST.MF");
Manifest manifest = new Manifest(inputStream);

Please note that running Tomcat from Eclipse is not the same as running Tomcat alone as Eclipse plays with the classloader.

a bit late, but this works for me (web appl in Glassfish)

Properties prop = new Properties();
prop.load(getServletContext().getResourceAsStream("/META-INF/MANIFEST.MF"));
System.out.println("All attributes:" + prop.stringPropertyNames());
System.out.println(prop.getProperty("{whatever attribute you want}"));

Try to use jcabi-manifests, that does all this loading work for you. For example:

String version = Manifests.read("My-Version");

loads My-Version attribute from one of available MANIFEST.MF files.

Important to mention that (more details are here) in most web containers current thread class loader is not the same as servlet context class loader. That's why you should append your servlet context to the register in runtime (more info):

Manifests.append(servletContext);

Also, check this out: http://www.yegor256.com/2014/07/03/how-to-read-manifest-mf.html

The default way class loaders work is to defer to the parent before attempting to lookup their own resources. So if a parent class loader has any manifest available, that's what you'll get. In fact, app servers don't necessarily do this, to allow applications to override versions of libraries. Further, class loaders can have multiple jars and hence multiple manifests.

It may be able to get a resource URL of one of your uniquely named resource. Open a connection. Cast to JarURLConnection. Get the JarFile. Load the manifest from that. That may not work, particularly if Tomcat explodes the war.

[Update] Of course, the war file itself isn't on the classpath. The classpath will have something like WEB-INF/lib/(.jar|.zip) and WEB-INF/classes/. Getting a resource from the ServletContext should work.

Best solution: Do something different. :)