How can I execute a .jar file from the terminal

The . syntax can only be used to run (by "sourcing") shell scripts.

You'll need to use the java command to run a .jar file:

java -jar Minecraft.jar

If you don't have java installed, you can fix that by installing the default-jre¹ package. You can see if you already have java installed by running in a terminal:

java -version 

[1]: This will install the default openjdk Java runtime. You can use openjdk-8-jre, or openjdk-7-jre, or openjdk-6-jre instead, if you prefer - whichever is available on your version of Ubuntu.

Linux is perfectly capable of running a foreign binary, like a JAR file. This is how Wine works, for example. To run JAR files as executable do the following in a console

sudo apt-get install binfmt-support

Cd to your JAR file and change it to executable (you can also do this through file properties in Nautilus)

chmod a+rx myjar.jar

Run your jar file just as if it was any other binary executable or shell script

./myjar.jar

Note: Be sure you have binfmt_misc linux kernel module loaded. If you use your custom compiled kernel without this module, binfmt-support won't work.

If it is an executable jar, then

java -jar Minecraft.jar 

Not all jar-Archives contain an executable class, declared to be started in the Manifest file, but if there is, this will work.

Btw.: You don't start most programs from the shell with the dot. The dot is a shortcut for source, and it only works in the bash and some other shells, to include a script in the scope of the current session.

A compiled binary xybin is simply started with its name if it is in the path:

xybin 

or, with its absolute path:

/home/foo/proj/test/xybin

or with its relative path:

proj/test/xybin

or if you happen to be in the directory of the file, with this relative path:

./xybin

The file has to be marked executable for you (see: chmod). All of the above is true for shellscripts too, but they often have an extension .sh, and you can start a shellscript by invoking the interpreter, and then it needn't be marked executable:

 bash xy.sh

If you don't want to start a new bash, you can use source, and you do so, to consume function definitions, aliases and variable settings.