Following project structure:

spm-gwt
spm-server

spm-gwt is a module, spm-server is a webserver project.

spm-gwt has a dependency to module A, version 1.2
spm-server has a dependency to module A, version 1.1

When generating org.eclipse.wst.common.component, both versions of module A are included, and thus both files are copied to the web-inf/lib directory.

Actually, conflict resolution doesn't work correctly here, as the generated file fetches all libraries directly from module A.

Probably it would be better to not transitively include all those libraries, but instead use the runtime configuration of spm-server and add all those libraries to the org.eclipse.wst.common.component file.