Jar command for extract and combine file  in Java

Dear Expert,
Question-1 I have some jar extract and combin files question and use the help from  this link at http://java.sun.com/j2se/1.5.0/docs/tooldocs/windows/jar.html#argfiles. But I extract
 files , for example, the jar file at the  link at http://mirrors.ibiblio.org/pub/mirrors/maven2/milyn/j2ee/1.4/j2ee-1.4.jar    by command
jar xf j2ee-1.4jar  that will create one directory called javax. And then I do the reverse by the command
jar cvf  junk.jar javax, junk.jar is created but its size is 789k which is totaly different from orginal one of 1668k
from j2ee-1.4.jar. Because I could NOT  attach my jar file into exchange-expert link, so I made this j2ee-1.4.jar as my similar problem. COuld you tell me why whether I use wrong option on jar command
Suppose both file size of junk.jar and j2ee-1.4.jar is same  
Question-2: I don't understand actully meaning of manifest . What is its pupose for Jar proccess, Just
from websearch  explain this with "  Manifest is an XML based, database driven Content Management System (CMS) for satisfying corporate communications needs, including Internet and Intranet"
Question-3, please possilbe, please download the file to test it at your side

Please advise it kindly
Duncan



http://mirrors.ibiblio.org/pub/mirrors/maven2/milyn/j2ee/1.4/j2ee-1.4.jar