How to express dependency in maven on java ee features for transition to Java 9?

The Module System speaks of the way the unnamed modules as in your case of loading the application from classpath constructs the module graph. Further, from the documentation itself:-

When the compiler compiles code in the unnamed module, or the java
launcher is invoked and the main class of the application is loaded
from the class path into the unnamed module of the application class
loader, then the default set of root modules for the unnamed module is
computed as follows:

• The java.se module is a root, if it exists. If it does not exist then
  every java.* module on the upgrade module path or among the system
  modules that exports at least one package, without qualification, is a
  root.

• Every non-java.* module on the upgrade module path or among the system
  modules that exports at least one package, without qualification, is
  also a root.

Otherwise, the default set of root modules depends upon the phase:

• At compile time it is usually the set of modules being compiled (more
  on this below);

• At link time it is empty; and

• At run time it is the application’s main module, as specified via the
  --module (or -m for short) launcher option.

It is occasionally necessary to add modules to the default root set in
order to ensure that specific platform, library, or service-provider
modules will be present in the module graph. In any phase the option

--add-modules <module>(,<module>)* where <module> is a module name, adds the named modules to the default set of root modules.

Similar issue was faced in jetty.project where a thread from jdk mailing list discussed over the same and the fix was to use:

--add-modules java.se.ee

which provided them access to all Java SE modules and in your case shall simply be:

--add-modules java.xml.bind

To use this in maven, you can embed the same to the maven-compiler-plugin
using

<compilerArgs>
    <arg>--add-modules</arg>
    <arg>java.xml.bind</arg>
</compilerArgs>

as suggested by ZhekaKozlov here.

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An important point to note is that marking deprecation of an API also means you might probably want to get away from using it. To adapt to this way you can probably start consuming the dependency on jaxb-api:2.3.0 which can now be loaded as a module and can be executed from the classpath as well. The change you need to make is to add the following to your dependencies list:

<dependency>
    <groupId>javax.xml.bind</groupId>
    <artifactId>jaxb-api</artifactId>
    <version>2.3.0</version>
</dependency>

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Update:- Eventually, with Java-10 already out and JDK/11 up next, one should ideally follow the link to JEP 320: Remove the Java EE and CORBA Modules and further replace such dependencies with their standalone libraries instead.