Currently the XHTML doesn't contain links, although PDFBox parses them. I'm new to Tika and haven't done java for 6 years, but someone more experienced could probably do this in a few hours.
The PDF2XHTML method loops through the annotations.
I found some code for dealing with links in annotations:
It involves checking the class.
I hope this helps someone.
|Field||Original Value||New Value|
|Fix Version/s||1.2 [ 12320169 ]|
|Fix Version/s||1.1 [ 12318849 ]|
|Status||Open [ 1 ]||Resolved [ 5 ]|
|Resolution||Fixed [ 1 ]|
|Transition||Time In Source Status||Execution Times||Last Executer||Last Execution Date|
|73d 12h 44m||1||Nick Burch||27/Apr/12 15:01|