it started to report problems after processing for WEB-INF/lib/lucene-core-3.0.0.jar started inside org.jboss.tools.modeshape.rest_1.0.0.v201009071649N-M2/modeshape-web-jcr-rest-client-2.1-SNAPSHOT-jar-with-dependencies.jar

Processing nested file: WEB-INF/lib/lucene-core-3.0.0.jar
[pack200] STDOUT: Legacy package version
[pack200] STDOUT: not found: Utf8=Index
[pack200] STDOUT: in: Index Utf8 [4084] {
[pack200] STDOUT: 0: Utf8=

looks like lucene started to index something (see STDOUT messages after snipped above)

That's probably a reason of further instrumentation error

[echo] Applying Seam-gen Patch
[echo] Move emma jars to /home/eskimo/Projects/jbds-build-4.0.0.M2/jbds-build/4.0.0.M2/201009071649/tests/eclipse
[copy] Copying 1 file to /home/eskimo/Projects/jbds-build-4.0.0.M2/jbds-build/4.0.0.M2/201009071649/tests/eclipse
[echo] portlet,examples,smooks,esb,freemarker,birt,as,archives,hibernate-tools,common,jsf,jst,struts,seam,vpe,ws,modeshape,jmx,jbpm-convert,cdi
[echo] Run tests for portlet
[mkdir] Created dir: /home/eskimo/Projects/jbds-build-4.0.0.M2/jbds-build/4.0.0.M2/201009071649/tests/test-results/emma-coverage/portlet
[instr] processing instrumentation path ...

BUILD FAILED
/home/eskimo/Projects/jbds-build-4.0.0.M2/org.jboss.ide.eclipse.releng/builders/buildNightly.xml:18: The following error occurred while executing this line:
/home/eskimo/Projects/jbds-build-4.0.0.M2/org.jboss.ide.eclipse.releng/builders/build.xml:68: The following error occurred while executing this line:
/home/eskimo/Projects/jbds-build-4.0.0.M2/org.jboss.ide.eclipse.releng/builders/build.xml:27: The following error occurred while executing this line:
/home/eskimo/Projects/jbds-build-4.0.0.M2/org.jboss.ide.eclipse.releng/builders/build.xml:39: The following error occurred while executing this line:
/home/eskimo/Projects/jbds-build-4.0.0.M2/org.jboss.ide.eclipse.releng/builders/product/productBuild.xml:106: The following error occurred while executing this line:
/home/eskimo/Projects/jbds-build-4.0.0.M2/org.jboss.ide.eclipse.releng/builders/product/productBuild.xml:186: The following error occurred while executing this line:
/home/eskimo/Projects/jbds-build-4.0.0.M2/org.jboss.ide.eclipse.releng/builders/tests/testBuild.xml:142: The following error occurred while executing this line:
/home/eskimo/Projects/jbds-build-4.0.0.M2/org.jboss.ide.eclipse.releng/builders/tests/testBuild.xml:146: com.vladium.emma.EMMARuntimeException: com.vladium.emma.EMMARuntimeException

Solution is to exclude these jars from packing, using eclipse.inf files: http://wiki.eclipse.org/JarProcessor_Options