The following are what I consider "bad uses" of astools code. Not all are the fault of the consuming component. Some may be the fault of inadequate API on the part of astools.

Either way, here's the list:

ws/tests/org.jboss.tools.ws.creation.core.test/src/org/jboss/tools/ws/creation/core/test/command/AbstractJBossWSGenerationTest.java:import org.jboss.ide.eclipse.as.core.server.internal.JBossServer;
seam/plugins/org.jboss.tools.seam.core/src/org/jboss/tools/seam/internal/core/project/facet/Seam23FacetInstallDelegate.java:import org.jboss.ide.eclipse.as.core.modules.SingleDeployableFactory;
seam/plugins/org.jboss.tools.seam.core/src/org/jboss/tools/seam/internal/core/project/facet/ResourceDeployer.java:import org.jboss.ide.eclipse.as.core.modules.SingleDeployableFactory;
bpel/plugins/org.jboss.tools.bpel.runtimes/src/org/jboss/tools/bpel/runtimes/module/JBTBPELPublisher.java:import org.jboss.ide.eclipse.as.core.publishers.PublishUtil;
bpel/plugins/org.jboss.tools.bpel.runtimes/src/org/jboss/tools/bpel/runtimes/module/JBTBPELPublisher.java:import org.jboss.ide.eclipse.as.core.server.xpl.LocalCopyCallback;
bpel/plugins/org.jboss.tools.bpel.runtimes/src/org/jboss/tools/bpel/runtimes/module/JBTBPELPublisher.java:import org.jboss.ide.eclipse.as.core.server.xpl.PublishCopyUtil;
esb/tests/org.jboss.tools.esb.project.core.test/src/org/jboss/tools/esb/project/core/test/ESBProjectDeploymentTest.java:import org.jboss.ide.eclipse.as.core.server.internal.DeployableServer;
examples/plugins/org.jboss.tools.project.examples.cheatsheet/src/org/jboss/tools/project/examples/cheatsheet/actions/RunOnServer.java:import org.jboss.ide.eclipse.as.core.modules.SingleDeployableFactory;
maven/plugins/org.jboss.tools.maven.sourcelookup.ui/src/org/jboss/tools/maven/sourcelookup/ui/browsers/JBossSourceContainerDialog.java:import org.jboss.ide.eclipse.as.core.server.internal.JBossServer;
maven/plugins/org.jboss.tools.maven.sourcelookup.core/src/org/jboss/tools/maven/sourcelookup/containers/JBossSourceContainer.java:import org.jboss.ide.eclipse.as.core.server.bean.JBossServerType;
maven/plugins/org.jboss.tools.maven.sourcelookup.core/src/org/jboss/tools/maven/sourcelookup/containers/JBossSourceContainer.java:import org.jboss.ide.eclipse.as.core.server.bean.ServerBean;
maven/plugins/org.jboss.tools.maven.sourcelookup.core/src/org/jboss/tools/maven/sourcelookup/containers/JBossSourceContainer.java:import org.jboss.ide.eclipse.as.core.server.bean.ServerBeanLoader;
maven/plugins/org.jboss.tools.maven.sourcelookup.core/src/org/jboss/tools/maven/sourcelookup/containers/JBossSourceContainer.java:import org.jboss.ide.eclipse.as.core.server.internal.JBossServer;

Suggested fixes are as follows:
1) Make a JBossServer interface IJBossServer
2) Make serverbean official API
3) Make publish utils official API and try to separate htem from internal impl (difficult)