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Unfortunately this would just be due to the process of the Tomcat patch installation itself which we would not be able to modify. It's possible there may be switches that could be passed to the installer, but to do so with Protect you would need to set this up as a custom patch. Otherwise, you could also try disabling quiet install when deploying this so the path can be checked during install. This can be done by creating a custom deployment template and go into General > Deployment Actions > During > uncheck 'Quiet mode'.
You may want to look into contacting Apache about this or check their help (http://tomcat.apache.org/findhelp.html) to see if you can get some additional ideas.
I wanted to report it here as it seems to be the only app presented by Shavlik as valid for our environment, but breaks stuff when deployed. None of the other apps we patch with Shavlik (and we have hundreds) seem to have this type of issue. It may be suggested to not show this as a patch but as a software deployment as it does not patch correctly in all situations. Thanks for the input though.