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The ant editor should properly align a CDATA section while ignoring the text inside.
I'll do this in M9.
It will not be possible to resolve this issue without addressing bug 57379. This may be a good candidate for post 3.0.
The net result of this bug is that instead of leaving text inside CDATA sections untouched, the ant formatter will attempt to format it using the same rules that are applied to the rest of the build file, e.g. indenting xml elements, wrapping long lines, etc. As far as I know, unlike bug 54458 this bug does not entail any data loss, other than whitespace, formatting, etc.
With the fix that is in for bug 57379, all that remains is to fix the XmlDocumentFormatter. The XmlElementFormattingStrategy no longer messes with stuff inside CDATA sections.
Deferred to post 3.0
As of now 'LATER' and 'REMIND' resolutions are no longer supported. Please reopen this bug if it is still valid for you.
This bug seems to have been closed by some automatic process but it seems pretty valid to me. It's very annoying as soon as you start using CDATA like is required when doing multiline replace with Ant replace task.