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I cannot double click .jar files but I can run them through cmd

As far as I have figured out, I have to do something like this:
Open the Registry Editor, and navigate to HKEY_CLASSES_ROOT\jarfile\shell\open\command, and modify the value of the Default key as follows
Replace [Location of your JRE] in "[Location of your JRE]\bin\javaw.exe" -jar "%1" %* with the root directory of your JRE installation. For example, "C:\Program Files\Java\jre7\bin\javaw.exe" -jar "%1" %*.
Repeat the above steps for HKEY_LOCAL_MACHINE\SOFTWARE\Classes\jarfile\shell\open\command.
The problem is that I don't have that "jarfile".
I would appreciate any help.

The registry portion is basically notifying the OS that when you attempt to run the jar file what program to use, where it located and the arguements to specify opening a jar file with that application.
It you dont have javaw.exe then install java, if your talking about the "%1" %* then its just a way of saying run javaw.exe -jar "file.jar" where file.jar is the jar file you double clicked on. "%1" %* does not and will not exist as a file or object.

Java - No Main Manifest Attribute, in App.jar error even though MANIFEST.MF file is in /META-INF

I have been trying to get this to work, but it won't. I went through the Archive Manager and found the MANIFEST.MF file in App.jar/META-INF/ so I don't know why it says there isn't one!
chmod-ing it with chmod +x ./App.jar and running ./App.jar returns
bash: ./App.jar: cannot execute binary file: Exec format error
Running Linux Mint 20 (Based on Ubuntu 20.04) With OpenJDK 11.

Use java -jar App.jar to run the executable JAR file.
There is a way to make JAR files directly executable using the binfmt_misc kernel feature but most users/linux distributions don't bother to set it up.

How to run `jdeprscan` on an EAR

The jdeprscan tool determines lists all deprecated and non-existing dependencies. It can run on classes, directories and on a JAR.
But how to run it on an EAR ?

Inspired by https://stackoverflow.com/a/57217414/698168, I explode the EAR into JARs using the following script (Windows) :
rem remove previous run
rd /s /q ear
rem extract the EAR
"C:\Program Files\7-Zip\7z" x -oear *.ear
rem extract the WAR
cd ear
"C:\Program Files\7-Zip\7z" x -owar *.war
rem unify JAR from EAR and WAR
copy war\WEB-INF\lib\*.jar lib
rem make JAR with the classes
cd war\WEB-INF\classes
rem "C:\Program Files\7-Zip\7z" a -r my-app.jar
"C:\Program Files\Java\jdk-11\bin\jar" cvf my-app.jar -C . .
rem Note: using 7zip to create the JAR may lead to errors when running jdeprscan, thus we are using the jar command
copy my-app.jar ..\..\..
rem return to origin
cd ..\..\..
rem unpack all libraries...
cd lib
"C:\Program Files\7-Zip\7z" x -aoa -oclasses *.jar
rem .. and repack them as a fat JAR
cd classes
rem "C:\Program Files\7-Zip\7z" a -r 00lib.jar
"C:\Program Files\Java\jdk-11\bin\jar" cvf 00lib.jar -C . .
rem duplicate the fat JAR and make some cleaning
copy 00lib.jar ..\00lib.jar
copy 00lib.jar ..\01lib.jar
cd ..
rd /s /q classes
rem return to origin
cd ..\..
Note that this script does not use the librairies from the JEE Server (i.e. all the Maven librairies with scope "provided" will be reported as error: cannot find class by jdeprscan).
Then I generate a jdeprscan report using the following command :
"C:\Program Files\Java\jdk-11\bin\jdeprscan" --for-removal --verbose --class-path ear\lib\*.jar ear\my-app.jar > deprscan.log 2>&1
You can then inspect the jdeprscan.log file. The classes that are not found may not exist in the newest Java version (such as 11) or may be present in the JEE modules. A missing class looks like the following (BASE64Encoder is not provided anymore by Java 11 but is used by ChecksumHelper):
Processing class oracle/spatial/security/ChecksumHelper...
error: cannot find class sun/misc/BASE64Encoder
In the best case, you can find the JAR name above in the log file (e.g. Jar file my-lib-2.3.4.jar), otherwise you will need to determine the library from the class name.
Note: all the above was designed with the idea to migrate Java 8 to Java 11.

compile files from different directories with javac, referring a depending jar file?

I have the following set up:
I have 4 packages:
root/src/terminal - has some java files
root/src/mail - has some java files
root/src/data - has some java files
root/src/main - has a single java file, Main.java
I also have the following files
root/bin - a folder to store .class files
root/mail.jar - a jar file which has important classes used in my code
Within the root, I would like to enter a terminal command which compiles root/src/main/Main.java and puts the class files in the root/bin location.
Can someone show me the command to do this? I'm on a Mac (running Leopard).

Here's the one liner:
cd /xyz/root
rm -rf bin/*
javac -d bin -classpath mail.jar -sourcepath src main/Main.java
Alternatively, you could use absolute directory names:
rm -rf /xyz/root/bin/*
javac -d /xyz/root/bin -classpath /xyz/root/mail.jar \
-sourcepath /xyz/root/src /xyz/root/ main/Main.java
In reference to Ant you said "I would rather keep it simple.".
In fact in the long term it is simpler to create a simple Ant build.xml file. The alternative is a bunch of non-portable scripts or batch file ... or lots of typing.
To run the application, assuming that you are still in the /xyz/root directory:
java -classpath bin:mail.jar main.Main
Or on Windows:
java -classpath bin;mail.jar main.Main
Or modify the above to use absolute pathnames in the classpath argument; e.g.
java -classpath /xyz/root/bin:/xyz/root/mail.jar main.Main

Without knowing your operating system?
What you should look into is using Apache Ant. It is a build tool that once installed and configured can utilize a build.xml file in your root to compile class files to a folder as well as package a jar file.
http://ant.apache.org/

try this:
javac -cp "/root/mail.jar;/root/src;" -d "/root/bin" Main.java
This is written hoping that you have package declarations in your classes from src folder like package terminal; and package main;.
See this: Options in javac command
Or use Apache Ant as suggested by maple_shaft.
From comment give by #maple_shaft:
In Unix, Linux operating systems the classpath separator is a colon instead of a semicolon.

Java execute jar which depends on other jar from command line

I have an application that uses an external jar. I used eclipse and it works fine. I export as jar from eclipse, having created a Manifest file that has as Class-Path: ./cab.v1.jar
I place both jars in the same directory.
I run in command line:
java -jar myApp.jar
and get java.lang.NoClassDefFoundError for the classes in the cab.v1.jar (the other jar)
Have also tried java -cp . -jar myApp.jar but no success.
What am I doing wrong?

Using the documentation for the Manifest it does not use a ./ for relative directories. Try it just with:
Class-Path: cab.v1.jar
Note that the -cp option is ignored when using -jar.

If you use the -jar option the classpath is ignored. You could start the application by
java -cp jar1.jar:jar2.jar mainclass
The class path separator ':' is ';' on windows.