I very quickly browsed the (current) source for JarThemeFactory, and as the output you posted suggests that may be the origin of the problem. The logic in getThemeAttributes opens a connection using a URL and opens a stream using that connection. A finally block closes the stream but the connection seems to be left open.
I did not search for an existing issue against Woodstock for this, but you may want to open one if there isn't one already.
The advances in GlassFish V2 to deal with open JARs would help with this, but it's always better to get the underlying problem fixed.
- Tim
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