Problem:

There are a large number of errors in the error log after indexing of Eclipse help has completed.

Not all of them are shown, as they are all basically the same error:

!ENTRY org.eclipse.help.base 4 0 2014-03-18 15:51:59.938 !MESSAGE An error occured while pre-processing help XHTML document "/com.microfocus.eclipse.help.ed.windows/html/HRERRHSERRLA.html" for search indexing !STACK 0 org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; JAXP00010001: The parser has encountered more than "64000" entity expansions in this document; this is the limit imposed by the JDK.  at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown Source)  at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unknown Source)  at org.eclipse.help.internal.dynamic.DocumentReader.read(DocumentReader.java:56)  at org.eclipse.help.internal.dynamic.XMLProcessor.process(XMLProcessor.java:49)  at org.eclipse.help.internal.xhtml.DynamicXHTMLProcessor.process(DynamicXHTMLProcessor.java:76)  at org.eclipse.help.internal.search.XHTMLSearchParticipant.preprocess(XHTMLSearchParticipant.java:106)  at org.eclipse.help.search.SearchParticipantXML.addDocument(SearchParticipantXML.java:296)  at org.eclipse.help.internal.search.HTMLSearchParticipant.addDocument(HTMLSearchParticipant.java:51)  at org.eclipse.help.internal.search.SearchIndex.addDocument(SearchIndex.java:231)  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:671)  at org.eclipse.help.internal.search.LocalSearchManager.ensureIndexUpdated(LocalSearchManager.java:645)  at org.eclipse.help.internal.search.LocalSearchManager.search(LocalSearchManager.java:590)  at org.eclipse.help.internal.search.SearchManager.searchLocal(SearchManager.java:103)  at org.eclipse.help.internal.search.SearchManager.search(SearchManager.java:94)  at org.eclipse.help.internal.search.SearchProgressMonitor$2.run(SearchProgressMonitor.java:162)  at java.lang.Thread.run(Unknown Source)

!ENTRY org.eclipse.help.base 4 0 2014-03-18 15:52:06.832 !MESSAGE An error occured while pre-processing help XHTML document "/com.microfocus.eclipse.help.ed.windows/html/GUID-E08E00FA-EFB0-480B-894A-8060166787BC.html" for search indexing !STACK 0 org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 1; JAXP00010001: The parser has encountered more than "64000" entity expansions in this document; this is the limit imposed by the JDK.  at com.sun.org.apache.xerces.internal.parsers.DOMParser.parse(Unknown Source)  at com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderImpl.parse(Unknown Source)  at org.eclipse.help.internal.dynamic.DocumentReader.read(DocumentReader.java:56)  at org.eclipse.help.internal.dynamic.XMLProcessor.process(XMLProcessor.java:49)  at org.eclipse.help.internal.xhtml.DynamicXHTMLProcessor.process(DynamicXHTMLProcessor.java:76)  at org.eclipse.help.internal.search.XHTMLSearchParticipant.preprocess(XHTMLSearchParticipant.java:106)  at org.eclipse.help.search.SearchParticipantXML.addDocument(SearchParticipantXML.java:296)  at org.eclipse.help.internal.search.HTMLSearchParticipant.addDocument(HTMLSearchParticipant.java:51)  at org.eclipse.help.internal.search.SearchIndex.addDocument(SearchIndex.java:231)  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:671)  at org.eclipse.help.internal.search.LocalSearchManager.ensureIndexUpdated(LocalSearchManager.java:645)  at org.eclipse.help.internal.search.LocalSearchManager.search(LocalSearchManager.java:590)  at org.eclipse.help.internal.search.SearchManager.searchLocal(SearchManager.java:103)  at org.eclipse.help.internal.search.SearchManager.search(SearchManager.java:94)  at org.eclipse.help.internal.search.SearchProgressMonitor$2.run(SearchProgressMonitor.java:162)  at java.lang.Thread.run(Unknown Source)

Resolution:

Please refer to https://community.oracle.com/thread/2594170 as this issue appears to be a bug in the JDK. (https://bugs.openjdk.java.net/browse/JDK-8028111).

The links discuss a workaround, but the ultimate solution is to upgrade to JRE7_U55 or later where the bug is fixed.