Take a look at uncle Bob’s Package Design Principles. He explains reasons and motivations behind those principles, which I have elaborated on below:
Classes that get reused together should be packaged together so that the package can be treated as a sort of complete product available for you. And those which are reused together should be separated away from the ones those are not reused with. For example, your Logging utility classes are not necessarily used together with your file io classes. So package all logging them separately. But logging classes could be related to one another. So create a sort of complete product for logging, say, for the want of better name commons-logging package it in a (re)usable jar and another separate complete product for io utilities, again for the want of better name, say commons-io.jar.
If you update say commons-io library to say support java nio, then you may not necessarily want to make any changes to the logging library. So separating them is better.
Now, let’s say you wanted your logging utility classes to support structured logging for say some sort of log analysis by tools like splunk. Some clients of your logging utility may want to update to your newer version; some others may not. So when you release a new version, package all classes which are needed and reused together for migration. So some clients of your utility classes can safely delete your old commons-logging jar and move to commons-logging-new jar. Some other clients are still ok with older jar. However no clients are needed to have both these jars (new and old) just because you forced them to use some classes for older packaged jar.
Avoid cyclic dependencies. a depend on b; b on c; c on d; but d depends on a. The scenario is obviously deterring as it will be very difficult to define layers or modules, etc and you cannot vary them independly relative to each other.
Also, you could package your classes such that if a layer or module changes, other module or layers do not have to change necessarily. So, for example, if you decide to go from old MVC framework to a rest APIs upgrade, then only view and controller may need changes; your model does not.