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I'm pretty familliar with .NET and know that patches and upgrades are mutually exclusive to framework versions (1.x) and (2.x / 3.x) and (4.x). This segregation makes it easy to understand the dependencies.

What logic or segregation applies to applying Java upgrades? When should I do it, or when should I not?

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As Always the answer is 'It Depends'.

If you are a consumer and the patch is security related do it now.

If you are an enterprise and you are running an application server and the patch details do not mention a security vulnerability that you are likely to hit (User running malicious JNLP application) you can hold off. If the 'patch' is adding new functionality such as Java 1.6.0 Update 10 (Update N) then you can maybe hold off.

In general updates to a certain Java version (1.4.2, 5, 6, 7) should be API stable and ok to update, but depending on what your application does to java you may need to test or hold off.

For instance recently Oracle changed some metadata about the HotSpot VM in a patch which caused the Eclipse IDE to fail.

99 times out of a 100 the Java patches should be API stable and have non-breaking changes.

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Many well-known versions of applications that require a specific java version usually include that version of java binaries with their application, and launching it is some variation of <-lots -of -switches>.

In the above case, upgrading the general/system-wide/default java usually has no impact on the application with it's own java binaries. On the other hand, you may also be unaware that the application-specific version of java (with a known vulnerability) exists when you update the system default java, unless you are actually measuring and reporting on it using a software inventory application.

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