Why are there duplicates of the same application link in config.xml?

I'm trying to debug a problem with application links between Jira 5.0.7, Fisheye 2.6.0 and Confluence 3.5.6. When I dug into the config.xml file on the fisheye server I found that there were multiple entries for each application I'd created a link for. For example, I'd created a link to the Jira server at and the Confluence server at During the debugging process I updated each link several times and a few times I deleted the link altogether and started over.

When I examined the config.xml file I found 17 trustedApplication entries for the jira application and 3 for the confluence application all with the same name, id and publicKey. I backed up the config.xml, made a change to the Application Link for the confluence server and compared the new config.xml file to the backup. Lo and behold, there was a 4th trustedApplication entry for the confluence server.

It's worth noting that there's nothing in the config.xml file to indicate if a given trustedApplication entry is for incoming or outgoing authentication. I figured that each trustedApplication entry would either have a section for incoming and outgoing or there would be exactly two entries for a given trustedApplication, each one being either incoming or outgoing.

Is there a compelling reason for this behavior? Or have I found a bug in Fisheye? More importantly, is it safe to delete any of the trustedApplication entries in the config.xml file?

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After a bunch of research (read: poking at it with a stick), I found that all the entries are for incoming connections, as the outgoing connection settings are pulled from the remote server. The old entries can be deleted without any problems. The same behavior exists in Confluence as well, but the trustedApplication entries are stored in the database and are (for want of a better word) disabled when no longer in use. My best bet is that the entries are stored in the config.xml so there's some level of backup.

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