Use of help docs causes lucene 5 index errors in console log

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.565
!MESSAGE Error trying to consume Lucene index from bundle org.eclipse.jst.ws.consumption.ui.doc.user_1.0.700.v201610271000 [429]. Please use an index built with Lucene 5 or higher.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.610
!MESSAGE Help index declared, but missing for plugin org.eclipse.dstore.doc.isv.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.616
!MESSAGE Help index declared, but missing for plugin org.eclipse.platform.doc.isv.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.638
!MESSAGE Error trying to consume Lucene index from bundle org.eclipse.jst.ws.axis2.ui.doc.user_1.0.200.v201610271000 [425]. Please use an index built with Lucene 5 or higher.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.638
!MESSAGE Help index declared, but missing for plugin org.eclipse.jdt.doc.user.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.640
!MESSAGE Error trying to consume Lucene index from bundle org.eclipse.wst.command.env.doc.user_1.5.400.v201610271000 [455]. Please use an index built with Lucene 5 or higher.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.675
!MESSAGE Error trying to consume Lucene index from bundle org.eclipse.wst.dtdeditor.doc.user_1.0.700.v201610271000 [487]. Please use an index built with Lucene 5 or higher.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.676
!MESSAGE Help index declared, but missing for plugin org.eclipse.jdt.doc.isv.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.678
!MESSAGE Help index declared, but missing for plugin org.eclipse.platform.doc.user.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.680
!MESSAGE Error trying to consume Lucene index from bundle org.eclipse.jst.j2ee.doc.user_1.1.400.v201610271000 [392]. Please use an index built with Lucene 5 or higher.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.687
!MESSAGE Error trying to consume Lucene index from bundle org.eclipse.wst.xmleditor.doc.user_1.0.700.v201610271000 [554]. Please use an index built with Lucene 5 or higher.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.697
!MESSAGE Error trying to consume Lucene index from bundle org.eclipse.wst.xsdeditor.doc.user_1.0.800.v201610271000 [557]. Please use an index built with Lucene 5 or higher.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.707
!MESSAGE Error trying to consume Lucene index from bundle org.eclipse.jst.ejb.doc.user_1.1.301.v201610271000 [387]. Please use an index built with Lucene 5 or higher.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.715
!MESSAGE Error trying to consume Lucene index from bundle org.eclipse.jst.ws.axis.ui.doc.user_1.1.200.v201610271000 [418]. Please use an index built with Lucene 5 or higher.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.716
!MESSAGE Error trying to consume Lucene index from bundle org.eclipse.wst.wsdl.ui.doc.user_1.0.850.v201610271000 [467]. Please use an index built with Lucene 5 or higher.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.725
!MESSAGE Error trying to consume Lucene index from bundle org.eclipse.wst.webtools.doc.user_1.0.500.v201610271000 [543]. Please use an index built with Lucene 5 or higher.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.733
!MESSAGE Error trying to consume Lucene index from bundle org.eclipse.wst.server.ui.doc.user_1.1.600.v201610271000 [658]. Please use an index built with Lucene 5 or higher.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.738
!MESSAGE Help index declared, but missing for plugin org.eclipse.pde.doc.user.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.745
!MESSAGE Error trying to consume Lucene index from bundle org.eclipse.jst.ws.doc.user_1.0.700.v201610271000 [439]. Please use an index built with Lucene 5 or higher.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.747
!MESSAGE Help index declared, but missing for plugin org.eclipse.rse.doc.isv.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.749
!MESSAGE Error trying to consume Lucene index from bundle org.eclipse.wst.wsi.ui.doc.user_1.0.750.v201610271000 [471]. Please use an index built with Lucene 5 or higher.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.760
!MESSAGE Error trying to consume Lucene index from bundle org.eclipse.wst.sse.doc.user_1.1.100.v201610271000 [536]. Please use an index built with Lucene 5 or higher.

!ENTRY org.eclipse.help.base 4 0 2016-11-17 16:56:06.762
!MESSAGE Error trying to consume Lucene index from bundle org.eclipse.jst.server.ui.doc.user_1.0.600.v201610271000 [649]. Please use an index built with Lucene 5 or higher.
java.net.URISyntaxException: Illegal character in path at index 56: localhelp:/org.eclipse.mylyn.wikitext.help.ui/help/Mylyn WikiText User Guide.html?lang=en_CA
	at java.net.URI$Parser.fail(URI.java:2848)
	at java.net.URI$Parser.checkChars(URI.java:3021)
	at java.net.URI$Parser.parseHierarchical(URI.java:3105)
	at java.net.URI$Parser.parse(URI.java:3053)
	at java.net.URI.<init>(URI.java:588)
	at java.net.URL.toURI(URL.java:939)
	at org.eclipse.help.internal.base.util.ProxyUtil.getProxy(ProxyUtil.java:57)
	at org.eclipse.help.internal.base.util.ProxyUtil.getConnection(ProxyUtil.java:108)
	at org.eclipse.help.internal.base.util.ProxyUtil.getStream(ProxyUtil.java:124)
	at org.eclipse.help.internal.search.HTMLSearchParticipant.isXHTML(HTMLSearchParticipant.java:108)
	at org.eclipse.help.internal.search.HTMLSearchParticipant.addDocument(HTMLSearchParticipant.java:47)
	at org.eclipse.help.internal.search.SearchIndex.addDocument(SearchIndex.java:248)
	at org.eclipse.help.internal.search.IndexingOperation.addDocuments(IndexingOperation.java:252)
	at org.eclipse.help.internal.search.IndexingOperation.addNewDocuments(IndexingOperation.java:159)
	at org.eclipse.help.internal.search.IndexingOperation.execute(IndexingOperation.java:106)
	at org.eclipse.help.internal.search.LocalSearchManager.updateIndex(LocalSearchManager.java:630)
	at org.eclipse.help.internal.search.LocalSearchManager.ensureIndexUpdated(LocalSearchManager.java:604)
	at org.eclipse.help.internal.search.federated.IndexerJob.run(IndexerJob.java:32)
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
java.net.URISyntaxException: Illegal character in path at index 56: localhelp:/org.eclipse.mylyn.wikitext.help.ui/help/Mylyn WikiText User Guide.html?lang=en_CA
	at java.net.URI$Parser.fail(URI.java:2848)
	at java.net.URI$Parser.checkChars(URI.java:3021)
	at java.net.URI$Parser.parseHierarchical(URI.java:3105)
	at java.net.URI$Parser.parse(URI.java:3053)
	at java.net.URI.<init>(URI.java:588)
	at java.net.URL.toURI(URL.java:939)
	at org.eclipse.help.internal.base.util.ProxyUtil.getProxy(ProxyUtil.java:57)
	at org.eclipse.help.internal.base.util.ProxyUtil.getConnection(ProxyUtil.java:108)
	at org.eclipse.help.internal.base.util.ProxyUtil.getStream(ProxyUtil.java:124)
	at org.eclipse.help.search.SearchParticipantXML.addDocument(SearchParticipantXML.java:308)
	at org.eclipse.help.internal.search.HTMLSearchParticipant.addDocument(HTMLSearchParticipant.java:53)
	at org.eclipse.help.internal.search.SearchIndex.addDocument(SearchIndex.java:248)
	at org.eclipse.help.internal.search.IndexingOperation.addDocuments(IndexingOperation.java:252)
	at org.eclipse.help.internal.search.IndexingOperation.addNewDocuments(IndexingOperation.java:159)
	at org.eclipse.help.internal.search.IndexingOperation.execute(IndexingOperation.java:106)
	at org.eclipse.help.internal.search.LocalSearchManager.updateIndex(LocalSearchManager.java:630)
	at org.eclipse.help.internal.search.LocalSearchManager.ensureIndexUpdated(LocalSearchManager.java:604)
	at org.eclipse.help.internal.search.federated.IndexerJob.run(IndexerJob.java:32)
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)

!ENTRY org.eclipse.help.base 4 4 2016-11-17 16:56:20.057
!MESSAGE Help documentation could not be indexed completely.
!SUBENTRY 1 org.eclipse.help.base 4 4 2016-11-17 16:56:20.057
!MESSAGE Help document /org.eclipse.platform.doc.isv/reference/api/org/eclipse/ui/ide/undo/package-summary.html cannot be opened.
!SUBENTRY 1 org.eclipse.help.base 4 4 2016-11-17 16:56:20.057
!MESSAGE Help document /org.eclipse.jdt.doc.isv/reference/api/org/eclipse/jdt/debug/ui/launchConfigurations/package-summary.html cannot be opened.
!SUBENTRY 1 org.eclipse.help.base 4 4 2016-11-17 16:56:20.057
!MESSAGE Help document /org.eclipse.platform.doc.isv/reference/api/org/eclipse/ui/activities/package-summary.html cannot be opened.
!SUBENTRY 1 org.eclipse.help.base 4 4 2016-11-17 16:56:20.057
!MESSAGE Help document /org.eclipse.jdt.doc.isv/reference/api/org/eclipse/jdt/core/jdom/package-summary.html cannot be opened.
!SUBENTRY 1 org.eclipse.help.base 4 4 2016-11-17 16:56:20.057
!MESSAGE Help document /org.eclipse.rse.doc.isv/reference/extension-points/org_eclipse_rse_core_systemTypeProviders.html cannot be opened.
!SUBENTRY 1 org.eclipse.help.base 4 4 2016-11-17 16:56:20.057

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