Build Agent Upgrade Failures After TC Server Upgrade (6.0.2)

We recently upgraded an instance of TeamCity on a Linux server from version 5.1.2 to 6.0.2 that is also hosting multiple build agents on the same physical server.  Unfortunately, the automatic build agent upgrade did not occur as planned so I resulted in updating agent software manually.  At this point, we were able to bring up build agents on the server but noticed that plugins are missing because almost all build configurations have become incompatible with those agents.

I found a thread which instructed a user to delete "plugins" directory from build agent home directory which i did but caused the same issue of build agent upgrade starting but failing according to the server.  Here is the thread im referencing:
http://devnet.jetbrains.net/message/5279090#5279090

Furthermore, I see that there is an issue tracker for implementing a better solution for build agent upgrades which is here:
http://youtrack.jetbrains.net/issue/TW-14542

At this point, I cannot upgrade my build agents automatically from the server because the process fails and I cannot download the archive format of build agent software because it does not contain all necessary plugins.

In addition,  I have also restarted TeamCity Server several times in hope that plugins would be extracted properly but to no luck.

I've attached output of "ls -lR" command for the following directory: */webapps/ROOT/update/plugins/...

I've also attached log files of one of the build agents installed on the same server as well as TeamCity Server log for reference.

At this point, what should I do to get my build configurations working as they were version 5.x?

Thank you in advance for the help,
Oscar Almendarez



Attachment(s):
error.log.zip
launcher.log.zip
teamcity-agent.log.zip
upgrade.log.zip
webroot-plugins.out.txt.zip
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Adding another log file since limited to number of inital uploads for thread...(TeamCity Server log file)...



Attachment(s):
teamcity-server.log.zip
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We have discussed the same issue in youtrack at http://youtrack.jetbrains.net/issue/TW-15592

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