Tool environment plugin lets you use "tools" in unusual ways, such as from shell scripts.
See JENKINS-4532 for motivation.
Some screenshots are better than a long discussion:
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This is what you define in the Jenkins configuration screen:
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This is how you use the plugin in a job:
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This is what you get:
Compared to Custom Tools Plugin the advantage is that you can use the tool in arbitrary ways, not just running an executable from it.