What these classes have in common with java project?
Only org.netbeans.modules.java.j2seproject.ui.J2SELogicalViewProvider$OpenManagersWeakListener is java j2seproject and the  org.netbeans.modules.java.freeform.AnnotationProcessingQueryImpl$R is the free form project.
The rest are not related to project at all. I will create separate issues for them later on.

Integrated into 'main-golden'
Changeset: http://hg.netbeans.org/main-golden/rev/4d49307c1300
User: Jaroslav Tulach <jtulach@netbeans.org>
Log: #200051: Various editor & java related classes whitelisted for now

"Profiling" snapshot showing who loads what violator:
http://netbeans.org/bugzilla/attachment.cgi?id=109525

Nothing in common with java project:

org.netbeans.lib.editor.codetemplates.storage.CodeTemplateSettingsImpl$OnExpandAction -> http://netbeans.org/bugzilla/show_bug.cgi?id=202976

org.netbeans.modules.ant.grammar.AntHighlightsLayerFactory not in snapshot (probably not loaded)

org.netbeans.modules.editor.deprecated.pre65formatting.LegacyFormattersProvider -> MimeDataProvider loaded by first mime lookup search. This is the legacy module which is not loaded until someone uses it. I've found that the XML is using it, I've created an issue http://netbeans.org/bugzilla/show_bug.cgi?id=202981.

org.netbeans.modules.editor.deprecated.pre65formatting.LegacyFormattersProvider$IndentReformatTaskFactoriesProvider the same as above but can be fixed by using beforeLookup, so I am going to fix it.

org.netbeans.modules.editor.deprecated.pre65formatting.LegacyFormattersProvider$IndentReformatTaskFactoriesProvider replaced by lightweight ProxyLookup subclass jet-main 38f563a409a4

jet-main 422ce6304962

org.netbeans.modules.gsf.codecoverage.CoverageHighlightsLayerFactory caused by wrong registration in php.project and maven.coverage
fixed jet-main 7d1b9f860db5

The org.netbeans.modules.html.editor.indexing.HtmlIndexer$Factory and org.netbeans.modules.j2ee.persistence.indexing.CopyResourcesIndexer$Factory are newly added indexers loaded by SourceIndexers - duplicate of http://netbeans.org/bugzilla/show_bug.cgi?id=187271 which was created for some older Factories.

org.netbeans.modules.java.freeform.AnnotationProcessingQueryImpl$R is not loaded. Neither in snapshot nor found during test run, removing from wl, jet-main ad6b06ec2aac

org.netbeans.modules.java.hints.bugs.UnusedAssignmentOrBranch$HighlightsFactoryImpl  fixd jet-main 08e7235f44d0

The org.netbeans.modules.java.hints.bugs.UnusedAssignmentOrBranch$JavaFactoryImpl is a new class which needs to be loaded by JavaCustomIndexer which initializes JavaSourceTaskFactories and loads the task factory.

The org.netbeans.modules.java.j2seproject.ui.J2SELogicalViewProvider$OpenManagersWeakListener is a new class in the J2SELogicalViewProvider. It's obviously loaded as the J2SE logical view is displayed when the project is opened. The class is a weak listener listening on LibraryManager.getOpenManagers() and was introduce as a part of fix of issue #195942.

org.netbeans.modules.javadoc.highlighting.Factory wrongly registered in the MIMELookup, fixed jet-main c61702f1bbf5

The org.netbeans.modules.javawebstart.JWSLookupProvider, org.netbeans.modules.javawebstart.ui.customizer.JWSProjectProperties fixed in jet-main 90aa6b7fd5ac.
The JWSLookupProvider was replaced by directly registering JWSOpenProjectHook by @PSP which delays loading to point when it's needed (the project is opened) the JWSOpenProjectHook is loaded as the J2SEProject is opened but it's loaded later than the JWSLookupProvider was loaded.
Regarding the JWSProjectProperties it's quite complex class which was loaded due to isTrue call, fixed.

org.netbeans.modules.merge.builtin.visualizer.MergeHighlightsLayerFactory fixed jet-main f2a2d31a222d

org.netbeans.modules.mobility.editor.ConfigurationHighlightsLayerFactory fixed jet-main ff495de68a1a

The org.netbeans.modules.profiler.AbstractProjectTypeProfiler, org.netbeans.modules.profiler.j2se.J2SEProjectTypeProfiler, org.netbeans.modules.profiler.utils.ProjectUtilities, org.netbeans.modules.profiler.utils.ProjectUtilities$IntegrationUpdater are already fixed by Jarda B.
Fixing wl: jet-main 38ec57fab226

The org.netbeans.modules.projectimport.eclipse.core.spi.UpgradableProjectLookupProvider provides the ProjectOpenedHook which does Eclipse resync, if we want this feature we need the POH => WONTFIX.

Integrated into 'main-golden'
Changeset: http://hg.netbeans.org/main-golden/rev/38f563a409a4
User: Tomas Zezula <tzezula@netbeans.org>
Log: #200051:testWhitelist3 fails on java & editor related classes

For the typinghooks org.netbeans.spi.editor.typinghooks.DeletedTextInterceptor$Factory, org.netbeans.spi.editor.typinghooks.TypedBreakInterceptor$Factory,
org.netbeans.spi.editor.typinghooks.TypedTextInterceptor$Factory I've created a separate issue as it has really nothing in common with java project or java infrastructure. The factories are new interfaces and it seems that impls are wrongly registered in the MIMELookup. If they are using @MR they are already fixed by my previous fix of MR AP. If they are registered by hand they need to be corrected.
The issue number is #203151

Evaluated all wl violations. 

These are new classes which need to be loaded (marked as #200051 - valid loaded classes in the ide.kit/test/qa-functional/data/whitelist_3.txt):

org.netbeans.modules.editor.deprecated.pre65formatting.LegacyFormattersProvider
org.netbeans.modules.java.hints.bugs.UnusedAssignmentOrBranch$JavaFactoryImpl
org.netbeans.modules.java.j2seproject.ui.J2SELogicalViewProvider$OpenManagersWeakListener
org.netbeans.modules.javawebstart.JWSProjectOpenHook
org.netbeans.modules.projectimport.eclipse.core.spi.UpgradableProjectLookupProvider

a new issue for unrelated typinghooks was created, issue #203151
#203151 - whitelist3 is violated by TypingHooks
org.netbeans.spi.editor.typinghooks.DeletedTextInterceptor$Factory
org.netbeans.spi.editor.typinghooks.TypedBreakInterceptor$Factory
org.netbeans.spi.editor.typinghooks.TypedTextInterceptor$Factory

The rest was fixed.
Fixed jet-main d2cf19ba4c5c

Integrated into 'main-golden'
Changeset: http://hg.netbeans.org/main-golden/rev/90aa6b7fd5ac
User: Tomas Zezula <tzezula@netbeans.org>
Log: #200051:testWhitelist3 fails on java & editor related classes

Integrated into 'main-golden'
Changeset: http://hg.netbeans.org/main-golden/rev/90aa6b7fd5ac
User: Tomas Zezula <tzezula@netbeans.org>
Log: #200051:testWhitelist3 fails on java & editor related classes