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