Upgrades commons libraries to fix security vulnerabilities

[NicoPiel]

Updates several Apache Commons dependencies across modules to newer patch releases to fix security vulnerabilities.

Fixes #218

Notably upgrades
commons-lang3 (3.13.0 → 3.18.0),
commons-beanutils (1.9.4 → 1.11.0) and
commons-configuration2 (2.8.0 → 2.10.1), replacing old JARs with the updated artifacts.

[tonygermano]

There are references that need to be updated in /server/build.xml and /manager/ant-build.xml. Some of these libraries get added to the manifests of the launcher jars. I'm less concerned about /manager since we don't ship that, and it's probably going to be rewritten at some point, but since you are already updating the jars, you should probably update the build file to match.

Also, the /generator project should probably be kept up to date. That doesn't run on every build, but it is what creates https://github.com/OpenIntegrationEngine/engine/blob/main/server/lib/mirth-vocab.jar

I'd want to see the results of some people testing these changes and check if there are any documented compatibility issues with newer versions before we merge.

[NicoPiel]

There are references that need to be updated in /server/build.xml and /manager/ant-build.xml.

Done!

Also, the /generator project should probably be kept up to date.

Also Done!

[mgaffigan]

Old versions referenced in:

• donkey/.classpath
• donkey/lib/commons/commons-beanutils-1.9.4.jar
• donkey/lib/commons/commons-lang3-3.13.0.jar
• command/.classpath

[mgaffigan]

Are there libraries we ship that are depending on the three that are updated in this PR? Can we get those up to date at the same time? Approving regardless, since I don't see a downside to shipping as is.