I have a foo.war file (JSF web app). I unzipped it just fine.
unzip foo.war
Then meta-inf and web-inf folders are extracted. I made a change to a properties file inside of web-inf and I repackageed it as foo.war.
However below command I tried didn't do it. It left out package name and Java classes under it from classes folder.
zip foo.war META-INF/* WEB-INF/*