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Well we Identified all such jobs and cleaned the jobs where build.xml was missing However, today again we started getting warning for some other jobs.
I think some points made here http://jenkins-ci.361315.n4.nabble.com/What-is-those-quot-WARNING-Failed-to-inspect-quot-in-the-Jenkins-logs-td4689106.html discuss the issue in more details with possible reason why this could be happening.
Although we can ignore the warnings but overtime this takes toll on our heap and the application crashes. We do not any other error in jenkins log other than this before the application crashes. Please let me know if the above discussion does not help and if you need specific information which I can help with.