Veryfying Signed Jar files:

jarsigner -verify jar-file

https://docs.oracle.com/javase/tutorial/deployment/jar/verify.html
Signing jar files:
Your alias is "johndoe".
The keystore you want to use is in a file named "mykeys" in the current working
directory.
The TSA that you want to use to time stamp the signature is located at http://ts
a.url.example.com.
Under these assumptions, you could use this command to sign a JAR file named app
.jar:
jarsigner -keystore mykeys -tsa http://tsa.url.example.com app.jar johndoe
https://docs.oracle.com/javase/tutorial/deployment/jar/signing.html
Java 7u21 info:
http://www.oracle.com/technetwork/java/javase/tech/java-code-signing-1915323.htm
l
Java SE 7u21 will introduce changes to Java browser plug-in behavior, encouragin
g application authors and vendors to sign code with a certificate from a trusted
Certificate Authority. Developers are strongly encouraged to sign code now in p
reparation for this release and future releases. Details of the new security pr
ompts can be found in this java.com article.
Secutiry applets:
https://www.java.com/en/download/help/appsecuritydialogs.xml
Starting with 7u25, why is a signed JAR that previously worked fine now being fl
agged as unsigned?
Prior to 7u25, some components such as the index.list entry were allowed to be u
nsigned. As of 7u25, all contents of a JAR must be signed. Failure to do so will
trigger the unsigned code warning. To properly sign a jar, index entries must b
e created before the jar is signed. For more information see 8016771. -->
related: http://bugs.java.com/view_bug.do?bug_id=8016771
Solution: index.list must be signed
With 7u21 signed jars were allowed to be loaded without any unsigned warning if
they contain unsigned index.list entry but this is not true anymore with 7u25.
With 7u25 an extra unsigned warning message is shown if the jars are signing the
jars first and then try to add index entries inside it.
This issue can be resolved if changing the build routine:
1) Create all index entries first; index.list
2) Then try to sign all the jars

How to create index and other commands:

http://www.codejava.net/java-core/tools/using-jar-command-examples