In GRADLE-898 it has been fixed that the Eclipse plugin automatically adds source jars to the .classpath entries if they are available. But it does that only for the main artifact of the module, other jar artifacts in the same module are attached to the .classpath file but not their source files. I think that since it is legal to have multiple artifacts per module in Ivy and Gradle, the eclipse plugin should also handle multiple jar-source pairs. By the way, I have the same issue with the STS support for Gradle (which I use instead of Gradle Eclipse plugin), so I wonder if this is some system restriction of Gradle, the inability to maintain multiple jar-source pairs in single module?

As an example, consider module with the follwing ivy.xml descriptor:

<?xml version="1.0" encoding="UTF-8"?>
<ivy-module version="2.0" xmlns:m="http://ant.apache.org/ivy/maven">
<info organisation="com.etnetera.jnp"
module="jnp-core"
revision="3.6.3"
status="integration"
publication="20120502192549"
/>
<configurations>
...
</configurations>
<publications>
<artifact name="jnp-core" type="jar" ext="jar" conf="archives,compile"/>
<artifact name="jnp-core" type="source" ext="jar" conf="archives,sources" m:classifier="sources"/>
<artifact name="jnp-core-dict-single" type="jar" ext="jar" conf="archives,single"/>
<artifact name="jnp-core-dict-single" type="source" ext="jar" conf="archives,sources" m:classifier="sources"/>
...
</publications>
<dependencies>
...
</dependencies>
</ivy-module>

The resulting generated .classpath file is something like

...
<classpathentry kind="lib" path="C:/var/gradle/.../jnp-core-3.6.3.jar" sourcepath="C:/var/gradle/.../jnp-core-3.6.3-sources.jar" exported="true"/>
<classpathentry kind="lib" path="C:/var/gradle/.../jnp-core-dict-single-3.6.3.jar" exported="true"/>
...

That is, the module's main artifact is attached with its source artifact, but the secondary artifact is without source code.