I haven't studied this part yet, so I will post what I have learned from working with
Java and web apps, ok?
Q1 - jar files and war files mean different things, you really can rename a jar into a war and a war into a jar but they probably won't work.
You can say they are the same because the algorithm used to generate this files are the same (creating a jar is kind of zipping a folder) what changes is just the extension, but a war file represents a whole webapp, which means that the files inside a war file obeys the same structure as your application folder inside
tomcat for example. A jar file may represent a set of components and classes, like servlet-api.jar, you have got the whole servlet api in it and it's not an application.
Q2 and Q3 - If you put a war file inside tomcat's webapp folder, tomcat will treat it as a webapp and will try to start it (look for a WEB-INF folder, read the web.xml file, create a context, map the servlets, listeners and so on).
You will put jar files into WEB-INF/lib when this jars are used by your web application, like a custom jar with your set of classes, frameworks jar like log4j, hibernate or spring from example.
EARs files are used when you have more than one application (2 war files for exemple) and they need to share resources like jar files, property files or anything else so you don't need to duplicate this resources. EARs are sometimes used to keep things organized too.
Q4 - putting jar into WEB-INF/lib means that your webapp depends on this jars to work and that they are specifically to your webapp. The jars inside WEB-INF/lib will be in your webapp classpath when you deploy it, so when you generate a war file everithing inside the WEB-INF/lib will be packaged together.
hope this info helps and please post again if you didn't understand something.