Bug 1314319

I see the same thing.

!SESSION 2016-03-15 16:22:36.107 -----------------------------------------------
eclipse.buildId=4.5.1.v20160217-0100
java.version=1.8.0_72
java.vendor=Oracle Corporation
BootLoader constants: OS=linux, ARCH=x86_64, WS=gtk, NL=en_US
Command-line arguments:  -data file:/home/me/workspace/ -os linux -ws gtk -arch x86_64

!ENTRY net.sf.eclipsecs.core 4 0 2016-03-15 16:22:48.152
!MESSAGE Checkstyle-Plugin: Plug-in "net.sf.eclipsecs.core" was unable to instantiate class "net.sf.eclipsecs.core.projectconfig.filters.NonSrcDirsFilter".
!STACK 1
org.eclipse.core.runtime.CoreException: Plug-in "net.sf.eclipsecs.core" was unable to instantiate class "net.sf.eclipsecs.core.projectconfig.filters.NonSrcDirsFilter".
	at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.throwException(RegistryStrategyOSGI.java:194)
	at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:188)
	at org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension(ExtensionRegistry.java:905)
	at org.eclipse.core.internal.registry.ConfigurationElement.createExecutableExtension(ConfigurationElement.java:243)
	at org.eclipse.core.internal.registry.ConfigurationElementHandle.createExecutableExtension(ConfigurationElementHandle.java:55)
	at net.sf.eclipsecs.core.projectconfig.PluginFilters.<clinit>(PluginFilters.java:102)
	at net.sf.eclipsecs.core.projectconfig.ProjectConfigurationFactory.createDefaultProjectConfiguration(ProjectConfigurationFactory.java:142)
	at net.sf.eclipsecs.core.projectconfig.ProjectConfigurationFactory.loadFromPersistence(ProjectConfigurationFactory.java:165)
	at net.sf.eclipsecs.core.projectconfig.ProjectConfigurationFactory.getConfiguration(ProjectConfigurationFactory.java:81)
	at net.sf.eclipsecs.core.jobs.RunCheckstyleOnFilesJob.runInWorkspace(RunCheckstyleOnFilesJob.java:111)
	at org.eclipse.core.internal.resources.InternalWorkspaceJob.run(InternalWorkspaceJob.java:39)
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
Caused by: java.lang.NoClassDefFoundError: org/eclipse/jdt/core/JavaModelException
	at java.lang.Class.getDeclaredConstructors0(Native Method)
	at java.lang.Class.privateGetDeclaredConstructors(Class.java:2671)
	at java.lang.Class.getConstructor0(Class.java:3075)
	at java.lang.Class.newInstance(Class.java:412)
	at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:184)
	... 10 more
Caused by: java.lang.ClassNotFoundException: org.eclipse.jdt.core.JavaModelException cannot be found by net.sf.eclipsecs.core_6.5.0.201506170515
	at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:389)
	at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:352)
	at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:344)
	at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:160)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 15 more
!SUBENTRY 1 org.eclipse.equinox.registry 4 1 2016-03-15 16:22:48.153
!MESSAGE Plug-in "net.sf.eclipsecs.core" was unable to instantiate class "net.sf.eclipsecs.core.projectconfig.filters.NonSrcDirsFilter".
!STACK 0
java.lang.NoClassDefFoundError: org/eclipse/jdt/core/JavaModelException
	at java.lang.Class.getDeclaredConstructors0(Native Method)
	at java.lang.Class.privateGetDeclaredConstructors(Class.java:2671)
	at java.lang.Class.getConstructor0(Class.java:3075)
	at java.lang.Class.newInstance(Class.java:412)
	at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:184)
	at org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension(ExtensionRegistry.java:905)
	at org.eclipse.core.internal.registry.ConfigurationElement.createExecutableExtension(ConfigurationElement.java:243)
	at org.eclipse.core.internal.registry.ConfigurationElementHandle.createExecutableExtension(ConfigurationElementHandle.java:55)
	at net.sf.eclipsecs.core.projectconfig.PluginFilters.<clinit>(PluginFilters.java:102)
	at net.sf.eclipsecs.core.projectconfig.ProjectConfigurationFactory.createDefaultProjectConfiguration(ProjectConfigurationFactory.java:142)
	at net.sf.eclipsecs.core.projectconfig.ProjectConfigurationFactory.loadFromPersistence(ProjectConfigurationFactory.java:165)
	at net.sf.eclipsecs.core.projectconfig.ProjectConfigurationFactory.getConfiguration(ProjectConfigurationFactory.java:81)
	at net.sf.eclipsecs.core.jobs.RunCheckstyleOnFilesJob.runInWorkspace(RunCheckstyleOnFilesJob.java:111)
	at org.eclipse.core.internal.resources.InternalWorkspaceJob.run(InternalWorkspaceJob.java:39)
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
Caused by: java.lang.ClassNotFoundException: org.eclipse.jdt.core.JavaModelException cannot be found by net.sf.eclipsecs.core_6.5.0.201506170515
	at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:389)
	at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:352)
	at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:344)
	at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:160)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 15 more

!ENTRY org.eclipse.core.jobs 4 2 2016-03-15 16:22:48.186
!MESSAGE An internal error occurred during: "Checking files...".
!STACK 0
java.lang.NoClassDefFoundError: org/eclipse/jdt/core/JavaModelException
	at net.sf.eclipsecs.core.builder.CheckerFactory.<clinit>(CheckerFactory.java:91)
	at net.sf.eclipsecs.core.builder.Auditor.runAudit(Auditor.java:142)
	at net.sf.eclipsecs.core.builder.CheckstyleBuilder.handleBuildSelection(CheckstyleBuilder.java:300)
	at net.sf.eclipsecs.core.jobs.RunCheckstyleOnFilesJob.runInWorkspace(RunCheckstyleOnFilesJob.java:116)
	at org.eclipse.core.internal.resources.InternalWorkspaceJob.run(InternalWorkspaceJob.java:39)
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
Caused by: java.lang.ClassNotFoundException: org.eclipse.jdt.core.JavaModelException cannot be found by net.sf.eclipsecs.core_6.5.0.201506170515
	at org.eclipse.osgi.internal.loader.BundleLoader.findClassInternal(BundleLoader.java:389)
	at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:352)
	at org.eclipse.osgi.internal.loader.BundleLoader.findClass(BundleLoader.java:344)
	at org.eclipse.osgi.internal.loader.ModuleClassLoader.loadClass(ModuleClassLoader.java:160)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 6 more
	
Looks like something is going wrong in the static initializers are failing.

I just updated to the latest eclipse, but I still have this problem. 

Current eclipse packages:

$ rpm -qa|grep eclipse
eclipse-testng-6.8.6-6.fc23.noarch
eclipse-mylyn-docs-wikitext-3.18.0-2.fc23.noarch
eclipse-webtools-servertools-core-3.7.0-1.fc23.noarch
eclipse-remote-2.0.1-2.fc23.noarch
eclipse-webtools-sourceediting-3.7.0-1.fc23.noarch
eclipse-platform-4.5.2-4.fc23.x86_64
eclipse-filesystem-1.0-5.fc23.x86_64
eclipse-ecf-core-3.12.2-1.fc23.x86_64
eclipse-tm-terminal-4.0.0-3.fc23.noarch
eclipse-mylyn-3.18.0-2.fc23.noarch
eclipse-webtools-common-core-3.7.0-1.fc23.noarch
eclipse-pde-4.5.2-4.fc23.x86_64
eclipse-gef-3.10.1-1.fc23.noarch
maven-eclipse-plugin-2.9-14.fc23.noarch
eclipse-e4-importer-0.1.0-0.5.gite4610b6.fc23.noarch
eclipse-jdt-4.5.2-4.fc23.x86_64
eclipse-swt-4.5.2-4.fc23.x86_64
eclipse-findbugs-3.0.1-3.fc23.noarch
eclipse-cdt-8.8.0-6.fc23.x86_64
eclipse-egit-4.2.0-1.fc23.noarch
eclipse-jgit-4.2.0-2.fc23.noarch
eclipse-emf-runtime-2.11.2-1.fc23.noarch
eclipse-emf-core-2.11.2-1.fc23.x86_64
eclipse-findbugs-contrib-6.4.3-1.fc23.noarch
eclipse-rse-3.7.0-5.git97bd591.fc23.noarch
eclipse-webtools-servertools-3.7.0-1.fc23.noarch
devassistant-dap-eclipse-0.10.0dev-9.fc23.noarch
eclipse-checkstyle-6.5.0-2.fc23.noarch
eclipse-equinox-osgi-4.5.2-4.fc23.x86_64
eclipse-xsd-2.11.0-1.fc23.noarch
eclipse-webtools-common-3.7.0-1.fc23.noarch

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