As a paying customer we have access to the confluence sources. However we could not find the sources for the PDF export engine (version 4.1.3 key: com.atlassian.confluence.extra.flyingpdf).
As I understand it, the conversion of confluence pages to PDF takes 2 steps:
The source for flyingsaucer is available but we would be interested in the sources for the first part. Any hint would be welcome!
Right now the workaround on the issue you are experiencing (Confluence source distribution doesn't contain bundled plugin source code) is to open a support ticket. I opened one on your behalf so I can use the file sharing that comes with the support portal to supply the code.
Please watch for an email from the support portal.
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