Remove jars when updating packages

[rbouckaert]

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When installing a new package, currently any jar files in the lib directory remain there if not overwritten, and get loaded when BEAST, BEAUti etc start. This can cause problems when file names change between versions (e.g. MyPackage.addon.jar becomes MyPackage.package.jar) and can result in hard to diagnose problems. Therefore, when updating a package to a new version, the lib directory should be removed before unzipping the new package file.

[rbouckaert]

This is probably only an issue for installation by hand, or using ant for some packages, since the whole package directory gets deleted (including the lib directory) when updating a package.