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<plugin>
  <artifactId>maven-compiler-plugin</artifactId>
  <configuration>
    <source>1.4</source>
    <target>1.4</target>
  </configuration>
</plugin>

When I build a bundle, some classes are built in "target/classes" but they're not included in the final jar.

The only classes that will appear in the bundle are the ones you ask it to include using Export-Package, Private-Package, Include-Resource, and Embed-Dependency - so just because a file exists under target/classes does NOT mean it will end up in the bundle. This is because this is the way the underlying BND tool works (it is primarily pull-based).

Now the bundleplugin will look at your Maven project and add appropriate BND instructions to pull in resource files - and version 2.0.0 will also look at your source directory to set reasonable defaults for Export-Package and Private-Package (unless you set these yourself). So when using bundleplugin 2.0.0 I'd use the default Private-Package and Export-Package to begin with - I would then move towards using an explicit list of packages in Export-Package to add versioning, directives, etc.

The only time I would set Private-Package would be to have more control over what ends up in the bundle - either to remove certain packages or perhaps pull in additional packages not found by the source scanner. Also note that both Export-Package and Private-Package accept wildcards such as "org.example.*" which can reduce the number of entries in the list, but you should be careful not to set either the export or private instruction to "*" as this would pull in the entire classpath... dependencies and all!

How do I remove the generated Maven information from the resulting bundle JAR file?

Use the following archive setting:

<configuration>
  <archive>
    <addMavenDescriptor>false</addMavenDescriptor>
  </archive>
</configuration>

Put this in either the JAR or bundle plugin configuration.

Why do some generated resources (such as Declarative Services XML files) appear in the final jar, but others don't?

When you use the Service-Component instruction to specify Declarative Services the BND tool scans the project classpath for components and automatically adds its generated XML to the final bundle, therefore Include-Resource is not necessary. But if you generate files under OSGI-INF using another mechanism then they won't end up in the bundle unless you add that directory using Include-Resource (this goes back to the core design decision that BND pulls classes and resources into the bundle, rather than just taking everything under target/classes). We try to provide reasonable defaults on the Maven side in the bundleplugin so local classes and resources will end up in the bundle without additional configuration, but we do this by looking at the effective pom and src/ folder rather than the generated target/classes content.