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Sandboxing and AV's aside, if I wanted to manually look at/monitor my system for where they usually enter it, where could I look for possible malicious Java viruses/activity, e.g., would they first show in Task Manager or temp files?

Are there any tools for this?

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Manually monitoring for any kind of Malware is not exactly practical (even on a single computer, let alone in any kind enterprise setting). Also, the answer to that question will depend on what OS you are referring to.

I'm just going to assume you're using a windows OS. If you're really determined to conduct some kind of manual search, sort by date modified and look in directories that are common across all systems (system files, current user, program files, etc.).

As far as java vulnerabilities, just keep up to date on exploit notifications and keep your JVM updated.

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