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I noticed that some of the documentation changes in the UA area have been committed to HEAD but not to R4_HEAD. These need to be merged into R4_HEAD.
I just did a diff of R4_HEAD and master in platform.doc.user and platform.doc.isv. I was happy to find that there was only one difference. /org.eclipse.platform.doc.isv/guide/ua_help_setup_standalone.htm I noticed that there had been a merge of changes from HEAD into R4_HEAD on 6/2/11 which would explain the small number of discrepancies.
I have cherry picked the commit with message Bug 349851 - [Doc] Document -displayHelpWindow parameter to standalone help from master into R4_HEAD. Fixed.