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There seems to be a problem with the installer – although it seems to be an issue with Jenkins, not with the plugin. In my case, the extracted directory structure is missing several directory contents. However, if I extract the tarball myself, the directories are there. I have confirmed (via a unit test of the plugin) that even before the plugin starts deleting anything, the missing directories are not present. This is on Mac OS X.
The first example that I have run into consistently is the lib/node_modules/npm/node_modules/npmlog/node_modules directory: it is present in the tarball, and it can be extracted properly; however, it does not exist in the extracted tool directory. All the other files inside npmlog are present, it's just missing node_modules and children.
I'm still trying to find a reliable way to reproduce the issue. I'll also try updating the Jenkins hpi version requirement, to see if it was an issue that has been fixed in the Jenkins core.