As someone not very familiar with Java can someone expand on what he means by this: "Every library is usually packaged into its own JAR, and merging all dependencies into a single JAR, might cause collisions, especially with packaged resources (non-class files)."
A common example is with logging config files (e.g., logback.xml). Some libraries ship with their own (or a library's dependency). It's not uncommon in a large project to wind up with several logback.xml files littered around from libraries that included their own. These are called "resources" because they aren't code but they are included with the compiled distributable and are placed on the classpath. Of course, yo…
Speaking of Java logging, that's one area that drives me batty. The lack of a good standard Java logging library caused a multitude of logging libraries to be written. Different libraries then of course use different logging libraries, so each logging library generally has a way to wrap all the others, and they all work in different ways. Getting consistent and controllable logging (e.g. ability to turn on or off logging for a given thing) can sometimes be almost impossible to understand.