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I think this issue may be the root cause of problem I'm having with Jenkins 1.517. When using the native-maven-plugin in a Jenkins job, hudson.maven.reporters.MavenFingerprinter is leaving a file locked which System.gc() cleans up but in the interim causes "The process cannot access the file because it is being used by another process". Just putting a comment here in case someone else is affected by the issue. I'm going to try and upgrade to at least Jenkins 1.523 and see if the issue is resolved.
1.0-alpha-7 manifest goal mt.exe : general error c101008d: Failed to write the updated manifest to the resource of file The process cannot access the file because it is being used by another process
http://jira.codehaus.org/browse/MOJO-1941.