Embedded tomcat 7 servlet 3.0 annotations not working

    Tomcat tomcat = new Tomcat();
    tomcat.setPort(port);

    Context ctx = tomcat.addWebapp("/", new File(docBase).getAbsolutePath());
    StandardJarScanner scan = (StandardJarScanner) ctx.getJarScanner();
    scan.setScanClassPath(true);
    scan.setScanBootstrapClassPath(true); // just guessing here
    scan.setScanAllDirectories(true);
    scan.setScanAllFiles(true);

    tomcat.start();
    tomcat.getServer().await();

it works well for me using Tomcat Embed 7.0.90 from MVN

Well I finally solved it by looking in the Tomcat7 sources, namely in the unit tests that deal with EmbeddedTomcat and servlet 3.0 annotations.

Basically, you must start your Embedded Tomcat 7 like this to make it aware of your annotated classes:

String webappDirLocation = "src/main/webapp/";
Tomcat tomcat = new Tomcat();
tomcat.setPort(8080);

StandardContext ctx = (StandardContext) tomcat.addWebapp("/embeddedTomcat",
                new File(webappDirLocation).getAbsolutePath());

//declare an alternate location for your "WEB-INF/classes" dir:     
File additionWebInfClasses = new File("target/classes");
VirtualDirContext resources = new VirtualDirContext();
resources.setExtraResourcePaths("/WEB-INF/classes=" + additionWebInfClasses);
ctx.setResources(resources);

tomcat.start();
tomcat.getServer().await();

For the sake of clarity I should mention that this works for a standard Maven project where your "web resources" (such as static and dynamic pages, WEB-INF directory etc) are found in:

[your project's root dir]/src/main/webapp

and your classes get compiled into

[your project's root dir]/target/classes

(such that you'd have [your project's root dir]/target/classes/[some package]/SomeCompiledServletClass.class)

For other directories layouts, these locations need to be changed accordingly.

==== UPDATE: Embedded Tomcat 8 ====

Thanks to @kwak for noticing this.

The APIs have changed a bit, here how the above example changes when using Embedded Tomcat 8:

String webappDirLocation = "src/main/webapp/";
Tomcat tomcat = new Tomcat();
tomcat.setPort(8080);

StandardContext ctx = (StandardContext) tomcat.addWebapp("/embeddedTomcat",
                new File(webappDirLocation).getAbsolutePath());

//declare an alternate location for your "WEB-INF/classes" dir:     
File additionWebInfClasses = new File("target/classes");
WebResourceRoot resources = new StandardRoot(ctx);
resources.addPreResources(new DirResourceSet(resources, "/WEB-INF/classes", additionWebInfClasses.getAbsolutePath(), "/"));
ctx.setResources(resources);

tomcat.start();
tomcat.getServer().await();