Symptoms

After successfully logging into the application, users experience the following error on screen:

2010-10-25 21:13:05,336 ERROR [btpool0-5] org.mortbay.log org.mortbay.log.Slf4jLog-warn - Nested in javax.servlet.jsp.JspException: javax.el.ELException: com.atlassian.applinks.host.OsgiServiceProxyFactory$ServiceTimeoutExceeded: Timeout exceeded waiting for service - com.atlassian.applinks.spi.link.MutatingApplicationLinkService:
javax.el.ELException: com.atlassian.applinks.host.OsgiServiceProxyFactory$ServiceTimeoutExceeded: Timeout exceeded waiting for service - com.atlassian.applinks.spi.link.MutatingApplicationLinkService
at javax.el.BeanELResolver.getValue(BeanELResolver.java:298)
at javax.el.CompositeELResolver.getValue(CompositeELResolver.java:175)
at com.sun.el.parser.AstValue.getValue(AstValue.java:138)
at com.sun.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:206)

Cause

Multiple copies of Applinks and SAL plugin jars are present in your Fisheye installation. You can check for these plugin jars under your var/plugins/bundled/, var/plugins/user/ and lib/ directories.

Resolution

Remove the multiple copies of plugin jars from under your var/plugins/user/ and lib/ directories, ensuring that there is a single copy of each of them present, only under your var/plugins/bundled/ folder.
The list of jars present under var/plugins/bundled/ should be:

applinks-plugin-x.x.jar
sal-fisheye-plugin-x.x.jar (should ideally be the same version bundled with the FishEye release)

The list of jars present under lib/ should be:

applinks-api-x.x.jar 
applinks-host-x.x.jar
applinks-spi-x.x.jar
sal-spring-x.x.jar
sal-spi-x.x.jar
sal-api-x.x.jar

Apart from the above, also check the contents of your <FISHEYE_INST>/var/plugins/config/pluginstate.properties file to see whether there are any plugins reported to be in the "false" (disabled) state. If such entries are present , please remove them and check if that helps.

Further troubleshooting

If the problem persists, please contact Atlassian Support and attach the following information to the Support ticket:
1) A list of the jars in your var/plugins/bundled/, var/plugins/user/ and lib/ directories.
2) Uncomment the following block of lines from your /log4j.xml file:

<!--<logger name="com.atlassian.plugin">-->
        <!--<level value="debug"/>-->
        <!--<appender-ref ref="debuglog" />-->
        <!--<appender-ref ref="console" />-->
<!--</logger>-->

save and restart the instance.
This will log a lot of plugin related debug messages in the log file, which will give us more details.