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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.

Eclipse cannot find module even the module path is explicitly provided

I have created a module com.company.ep that is located in the source folder com.company.ep. (Yes, I have removed src from the build path and deleted it!) Inside the source folder, I have a couple of packages as the following:
com.company.ep <--- root source folder
com.company.ep.main <--- package 1
com.company.ep.model <--- package 2
com.company.ep.view <--- package 3
// ... more packages
module-info.java
The main class is located in the package com.company.ep.main.Main. In my module-info.java, I have configured the dependencies:
module com.company.ep {
exports com.company.ep.main;
exports com.company.ep.model;
exports com.company.ep.view;
// ... more exports
requires javafx.controls;
requires javafx.graphics;
}
When I tried to launch my program, eclipse told me that:
Error occurred during initialization of boot layer
java.lang.module.FindException: Module javafx.controls not found, required by com.company.ep
So, I tried to run it on the command prompt:
java -p d:\Applications\openjfx-sdk-11\lib;bin -m com.company.ep/com.company.ep.main.Main
bin is the output folder of eclipse, and it worked.
So, I went to Properties → Run/Debug Settings → Main → Show Command Line, it showed:
D:\Applications\openjdk-11.0.1\bin\javaw.exe -Dfile.encoding=UTF-8 -p "D:\Development\Eclipse-Workspace\MyProject\bin" -classpath "D:\Applications\openjfx-sdk-11\lib\javafx.base.jar;D:\Applications\openjfx-sdk-11\lib\javafx.controls.jar;D:\Applications\openjfx-sdk-11\lib\javafx.fxml.jar;D:\Applications\openjfx-sdk-11\lib\javafx.graphics.jar;D:\Applications\openjfx-sdk-11\lib\javafx.media.jar;D:\Applications\openjfx-sdk-11\lib\javafx.swing.jar;D:\Applications\openjfx-sdk-11\lib\javafx.web.jar;D:\Applications\openjfx-sdk-11\lib\javafx-swt.jar" -m com.company.ep/com.company.ep.main.Main
I have created a user library with all JARs added, and the library is added to the project's Modulepath.
Then I have tried to set the module path explicitly in VM arguments in Run/Debug Settings: -p D:\Applications\openjfx-sdk-11\lib, I'd still no luck.
My questions are:
Why javaw.exe?
Why classpath? As my library is added as a module-path entry.
How to configure the module dependencies in eclipse.
I am not sure if I have configured eclipse correctly, or whether it is probably a problem of OpenJDK as it worked when I worked on another computer with Oracle Java SE installed.
Thank you!

The explanation of why Eclipse fails on running your modular project can be found in the OpenJFX docs for Eclipse (modular from IDE section).
As it was already mentioned:
Being a modular project, and since we already added the JavaFX SDK library to the module-path, there is no need to add any VM arguments.
But if you run on Eclipse you will get the mentioned error:
Error occurred during initialization of boot layer
java.lang.module.FindException: Module javafx.graphics not found, required by hellofx
So why is it failing??
As explained in the docs:
This exception happens because the Eclipse ant task overrides the module-path
How does this happen??
Checking the command line applied (Show Command Line from Run Configurations...), you can find out why:
$JAVA_HOME/bin/java -Dfile.encoding=UTF-8 \
-p bin/hellofx \
-classpath $PATH_TO_FX \
-m hellofx/org.openjfx.MainApp
If you copy it and paste it and run it in a terminal, it will fail of course with the same message. The reason is that Eclipse doesn't add the JavaFX library to the module path.
If the task generates the wrong arguments, let's try to fix it by adding our own VM arguments by editing Run configurations... and adding -p $PATH_TO_FX:bin/hellofx.
But if you run it, it will fail again.
Let's check why, with Show Command Line from Run Configurations...
$JAVA_HOME/bin/java -Dfile.encoding=UTF-8 \
-p $PATH_TO_FX:bin/hellofx \
-p bin/hellofx \
-classpath $PATH_TO_FX \
-m hellofx/org.openjfx.MainApp
As you can see, the user's VM arguments are added before the default ant task arguments, so there are two -p (--module-path) options, and the first one (the user's one with the JavaFX jars) is overridden by the second one (only the project's module), so, again, the JavaFX jars are not added to the module path, and hence you get the error.
So how can we fix it??
As mentioned in the linked documentation, the possible fix is:
To prevent this issue click on Run -> Run Configurations... -> Java Application -> Dependencies, select Override Dependencies... and add -p /path-to/javafx-sdk-11/lib:bin/hellofx, and press Override.
With this solution, you can see it works, and you can check the command line:
$JAVA_HOME/bin/java -Dfile.encoding=UTF-8 \
-p $PATH_TO_FX:bin/hellofx \
-p bin/hellofx \
-classpath $PATH_TO_FX \
-p /path-to/javafx-sdk-11/lib:bin/hellofx \
-m hellofx/org.openjfx.MainApp
Basically we are adding again the "right" module path option, after all the failed ones.
While now the project runs, the solution is obviously not nice.
Here you can find a sample referred from the OpenJFX documentation.
EDIT
Based on #kleopatra comments, another workaround to make it work is the following:
For some reason, the library JavaFX11 (that contains modular jars) is not scanned and Eclipse doesn't include those jars into its -p option, but into the classpath:
$JAVA_HOME/bin/java -Dfile.encoding=UTF-8 \
-p bin/hellofx \
-classpath $PATH_TO_FX \
...
But, if you add those jars directly to the module path, it will do add them, and this will run fine:
$JAVA_HOME/bin/java -Dfile.encoding=UTF-8 \
-p bin/hellofx:$PATH_TO_FX/javafx.base.jar:...:$PATH_TO_FX/javafx.controls \
...
Then with this there is no more need to override the dependencies.
EDIT 2
As #mipa points out in a comment, there was a bug filed on this issue, and it has already been solved. I've tested it with Eclipse 2018-12 M2 (4.10.0M2) Build id: 20181108-1653, and it works with the JavaFX11 library only (as it should):
$JAVA_HOME/bin/java -Dfile.encoding=UTF-8 \
-p bin/hellofx:$PATH_TO_FX/javafx.base.jar:... \
-m hellofx/org.openjfx.MainApp

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.

How can I validate CSS on internal web pages?

I want to check internal web pages, so I cannot use the W3C validation service directly. I managed to run the XHTML validator locally, however, I have some problems with the css-validator. I do not really want to setup Tomcat or Jigsaw in order to be able to run Java servlet, and the commandline option gives me an error message
Exception in thread "main" java.lang.NoClassDefFoundError:
org.w3c.tools.resources.ProtocolException at
org.w3c.css.css.CssValidator.main(CssValidator.java:164)
How can I validate local CSS on a Linux box?

That jar is runnable, but it needs some extra libraries.
Examine the MANIFEST.MF file:
$ unzip -p css-validator.jar META-INF/MANIFEST.MF
Manifest-Version: 1.0
Ant-Version: Apache Ant 1.8.0
Created-By: 1.6.0_26-b03 (Sun Microsystems Inc.)
Main-Class: org.w3c.css.css.CssValidator
Class-Path: . lib/commons-collections-3.2.1.jar lib/commons-lang-2.6.j
ar lib/jigsaw.jar lib/tagsoup-1.2.jar lib/velocity-1.7.jar lib/xerces
Impl.jar lib/xml-apis.jar lib/htmlparser-1.3.1.jar
You need all the jars mentioned in Class-Path. You can download them from the maven repository using this script:
#!/bin/bash
set -e
mkdir -p lib
curl -LO http://www.w3.org/QA/Tools/css-validator/css-validator.jar
echo "\
http://repo1.maven.org/maven2/commons-collections/commons-collections/3.2.1/commons-collections-3.2.1.jar
http://repo1.maven.org/maven2/commons-lang/commons-lang/2.6/commons-lang-2.6.jar
http://repo1.maven.org/maven2/org/w3c/jigsaw/jigsaw/2.2.6/jigsaw-2.2.6.jar jigsaw.jar
http://repo1.maven.org/maven2/org/ccil/cowan/tagsoup/tagsoup/1.2/tagsoup-1.2.jar
http://repo1.maven.org/maven2/org/apache/velocity/velocity/1.7/velocity-1.7.jar
http://repo1.maven.org/maven2/xerces/xercesImpl/2.11.0/xercesImpl-2.11.0.jar xercesImpl.jar
http://repo1.maven.org/maven2/nu/validator/htmlparser/htmlparser/1.2.1/htmlparser-1.2.1.jar\
" | while read url shortname; do
if [ -z "$shortname" ]; then
shortname="${url##*/}"
fi
curl -L -o "lib/${shortname}" "${url}"
done
After doing that, it works:
$ java -jar css-validator.jar --output=soap12 file:badcss.html
{vextwarning=false, output=soap12, lang=en, warning=2, medium=all, profile=css3}
<?xml version='1.0' encoding="utf-8"?>
<env:Envelope xmlns:env="http://www.w3.org/2003/05/soap-envelope">
<env:Body>
<m:cssvalidationresponse
env:encodingStyle="http://www.w3.org/2003/05/soap-encoding"
xmlns:m="http://www.w3.org/2005/07/css-validator">
<m:uri>file:badcss.html</m:uri>
<m:checkedby>http://jigsaw.w3.org/css-validator/</m:checkedby>
<m:csslevel>css3</m:csslevel>
<m:date>2013-03-12T06:40:09Z</m:date>
<m:validity>false</m:validity>
<m:result>
<m:errors xml:lang="en">
<m:errorcount>1</m:errorcount>
<m:errorlist>
<m:uri>file:badcss.html</m:uri>
<m:error>
<m:line>8</m:line>
<m:errortype>parse-error</m:errortype>
<m:context> h1 </m:context>
<m:errorsubtype>
exp
</m:errorsubtype>
<m:skippedstring>
100%
</m:skippedstring>
<m:message>
Property fnt-size doesn't exist :
</m:message>
</m:error>
</m:errorlist>
</m:errors>
<m:warnings xml:lang="en">
<m:warningcount>1</m:warningcount>
<m:warninglist>
<m:uri>file:badcss.html</m:uri>
<m:warning>
<m:line>5</m:line>
<m:level>0</m:level>
<m:message>You should add a 'type' attribute with a value of 'text/css' to the 'style' element</m:message>
</m:warning>
</m:warninglist>
</m:warnings>
</m:result>
</m:cssvalidationresponse>
</env:Body>
</env:Envelope>

You can invoke the W3C validator from the command line:
Command-Line use
Any computer with Java installed can
also run the validator from the
terminal/console as a commandline
tool. Download the css-validator.jar
jar archive (or build it with ant jar)
and run it as :
java -jar css-validator.jar http://www.w3.org/
Note : the css-validator.jar file must
be located at the exact same level as
the lib/ folder to work properly.
Update: To get it to work, I checked out the full distribution from CVS and ran ant using the included build.xml. It downloaded all dependencies except for servlet.jar. To deal with that, I downloaded the binary distribution of Tomcat 6 and extracted it. Then, I edited the build.xml for css-validator to reflect the location of servlet.lib:
<property name="servlet.lib"
value="E:/Downloads/apache-tomcat-6.0.20/lib/servlet-api.jar"/>
Then ran ant again. This produced the css-validator.jar file in the top level of the directory checked out from CVS with the lib subdirectory containing the other jars it depends on. Then, I was able to run the validator successfully:
C:\Temp\validator\2002\css-validator> java -jar css-validator.jar http://www.unur.com/

For the lazy, here's a script I wrote to do what Sinan suggests:
#!/bin/sh
# W3C CSS Validator Install Script --------------
# installs W3C CSS Validator
# requires: ant, wget, javac
# see: http://jigsaw.w3.org/css-validator/DOWNLOAD.html
# see: http://esw.w3.org/CssValidator
# see: http://thecodetrain.co.uk/2009/02/running-the-w3c-css-validator-locally-from-the-command-line/
# see: http://stackoverflow.com/a/3303298/357774
##wget "http://www.w3.org/QA/Tools/css-validator/css-validator.jar"
#sudo aptitude install -y ant # uncomment if you don't have ant
CVSROOT=:pserver:anonymous:anonymous#dev.w3.org:/sources/public cvs checkout 2002/css-validator
mkdir 2002/css-validator/lib
TOMCAT6_VERSION='6.0.45'
wget "http://www.apache.org/dist/tomcat/tomcat-6/v$TOMCAT6_VERSION/bin/apache-tomcat-$TOMCAT6_VERSION.tar.gz"
tar xvf apache-tomcat-$TOMCAT6_VERSION.tar.gz
mv apache-tomcat-$TOMCAT6_VERSION/lib/servlet-api.jar 2002/css-validator/lib/servlet.jar
rm -rf apache-tomcat-$TOMCAT6_VERSION apache-tomcat-$TOMCAT6_VERSION.tar.gz
cd 2002/css-validator
ant jar
# usage example: java -jar css-validator.jar "http://csszengarden.com/"
That should work, at least until the next software dependency update breaks the ant build script (feel free to parameterize versions).
Hope this helps!

You can now use the new Linux command line tool htmlval for checking HTML and CSS. It should definitely work for validating local CSS on a Linux box.
Note: I'm the developer.