@zerwas: A .jar file can only be opened with the JRE if it's an
executable Jar file, i.e. if it has a Main-Class specification in its
manifest. If the Jar file doesn't have a main class specification, it
should be opened with the archive manager because it is not an
executable jar file. Opening a non-executable jar file using the JRE
would mean that as far as the user is concerned, nothing would happen as
the JRE would exit immediately. In terms of usability, this is actually
worse than opening all jar files with the archive manager.

@Pedro: I believe zerwas means that when a .jar file is double clicked, rather 
than being opened with the archive manager, it should be run using the 
following command:
java -jar /path/to/jar/file
This actually executes the Jar file, if and only if it contains a 
META-INF/MANIFEST.MF file that itself contains a line starting Main-Class: as 
explained here: http://www.cs.princeton.edu/introcs/85application/jar/jar.html

Having said this, I have reservation about being able to do run
executable jar files like this because it would mean that you could run
third party code contained in a jar file by just double clicking on it,
irrespective of whether the execute bit is set or not. In order not to
compromise security when doing this, you would need to run the JRE with
a restrictive security policy. Another alternative would be to treat
executable Jar files in a similar way to .deb files: open a dedicated
Java package installer that registers the Jar file as an application.

-- 
.jar file should open with JRE instead of archive manager
https://bugs.launchpad.net/bugs/607712
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