I am using jacoco 1.0.16 with Jenkins on a Apache Tomcat Server. The project I am building is a multiple module project using Maven. I build a parent project which then kicks off the test project (that has all the test classes). I get the error:

ERROR: Publisher hudson.plugins.jacoco.JacocoPublisher aborted due to exception
java.lang.IllegalStateException: basedir /home/irsmoper/.jenkins/jobs/irsm-test/builds/2015-03-19_13-59-11/jacoco/classes does not exist
at org.codehaus.plexus.util.DirectoryScanner.scan(DirectoryScanner.java:550)
at org.codehaus.plexus.util.FileUtils.getFileAndDirectoryNames(FileUtils.java:1717)
at org.codehaus.plexus.util.FileUtils.getFileNames(FileUtils.java:1645)
at org.codehaus.plexus.util.FileUtils.getFileNames(FileUtils.java:1627)
at org.codehaus.plexus.util.FileUtils.getFiles(FileUtils.java:1601)
at org.codehaus.plexus.util.FileUtils.getFiles(FileUtils.java:1584)
at hudson.plugins.jacoco.ExecutionFileLoader.analyzeStructure(ExecutionFileLoader.java:128)
at hudson.plugins.jacoco.ExecutionFileLoader.loadBundleCoverage(ExecutionFileLoader.java:137)
at hudson.plugins.jacoco.JacocoReportDir.parse(JacocoReportDir.java:102)
at hudson.plugins.jacoco.JacocoBuildAction.loadRatios(JacocoBuildAction.java:291)
at hudson.plugins.jacoco.JacocoBuildAction.load(JacocoBuildAction.java:273)
at hudson.plugins.jacoco.JacocoPublisher.perform(JacocoPublisher.java:371)
at hudson.tasks.BuildStepMonitor$3.perform(BuildStepMonitor.java:45)
at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:770)
at hudson.model.AbstractBuild$AbstractBuildExecution.performAllBuildSteps(AbstractBuild.java:734)
at hudson.maven.MavenModuleSetBuild$MavenModuleSetBuildExecution.post2(MavenModuleSetBuild.java:1037)
at hudson.model.AbstractBuild$AbstractBuildExecution.post(AbstractBuild.java:683)
at hudson.model.Run.execute(Run.java:1784)
at hudson.maven.MavenModuleSetBuild.run(MavenModuleSetBuild.java:529)
at hudson.model.ResourceController.execute(ResourceController.java:89)
at hudson.model.Executor.run(Executor.java:240)

I have tried to move files into the correct folders, but Jacoco keeps looking in that build folder, but the info it needs is in a different folder with source. When i moved the exec file into the correct folder, the build would complete, but no code coverage information was generated, and the console would still display:

[JaCoCo plugin] Number of found exec files: 0

I also tried pointing jacoco to the correct folders using ../../.. etc but it still did not work.

Same with me on Ubuntu 14.04, I get empty Code Coverage View but I get coverage with index.html published using HTML publisher plugin.
ERROR: Build step failed with exception
java.lang.IllegalStateException: basedir /var/lib/jenkins/jobs/Android_Build_TestCC/builds/22/jacoco/classes does not exist
at org.codehaus.plexus.util.DirectoryScanner.scan(DirectoryScanner.java:550)
at org.codehaus.plexus.util.FileUtils.getFileAndDirectoryNames(FileUtils.java:1717)
at org.codehaus.plexus.util.FileUtils.getFileNames(FileUtils.java:1645)
at org.codehaus.plexus.util.FileUtils.getFileNames(FileUtils.java:1627)
at org.codehaus.plexus.util.FileUtils.getFiles(FileUtils.java:1601)
at org.codehaus.plexus.util.FileUtils.getFiles(FileUtils.java:1584)
at hudson.plugins.jacoco.ExecutionFileLoader.analyzeStructure(ExecutionFileLoader.java:124)
at hudson.plugins.jacoco.ExecutionFileLoader.loadBundleCoverage(ExecutionFileLoader.java:133)
at hudson.plugins.jacoco.JacocoReportDir.parse(JacocoReportDir.java:102)
at hudson.plugins.jacoco.JacocoBuildAction.loadRatios(JacocoBuildAction.java:291)
at hudson.plugins.jacoco.JacocoBuildAction.load(JacocoBuildAction.java:273)
at hudson.plugins.jacoco.JacocoPublisher.perform(JacocoPublisher.java:371)
at hudson.tasks.BuildStepMonitor$1.perform(BuildStepMonitor.java:20)
at hudson.model.AbstractBuild$AbstractBuildExecution.perform(AbstractBuild.java:761)
at hudson.model.AbstractBuild$AbstractBuildExecution.performAllBuildSteps(AbstractBuild.java:721)
at hudson.model.Build$BuildExecution.post2(Build.java:183)
at hudson.model.AbstractBuild$AbstractBuildExecution.post(AbstractBuild.java:670)
at hudson.model.Run.execute(Run.java:1766)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
at hudson.model.ResourceController.execute(ResourceController.java:98)
at hudson.model.Executor.run(Executor.java:374)
Build step 'Record JaCoCo coverage report' marked build as failure
Finished: FAILURE