I am looking for a Java library to interface with standard Unix functions, i.e. stat(), getpwuid(), readlink().
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I would be surprised to see one, considering it would almost necessarily be platform-specific. Java is not the best tool for that job. But you could certainly hook in via JNI or calls out to external programs if you insist. Or perhaps look into Groovy, which I understand is reasonably good for shell scripting, though I have no personal experience with it.