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How does java find .class files of java standard library or libraries I buy

I came across this question:
What is a classpath and how do I set it?
and the first answer explainns what classpath is and how to set it:
.....First, let's suppose that MyClass is something you built as part of
your project, and it is in a directory in your project called output.
The .class file would be at
output/org/javaguy/coolframework/MyClass.class (along with every other
file in that package). In order to get to that file, your path would
simply need to contain the folder 'output', not the whole package
structure, since your import statement provides all that information
to the VM.
Now let's suppose that you bundle CoolFramework up into a .jar file,
and put that CoolFramework.jar into a lib directory in your project.
You would now need to put lib/CoolFramework.jar into your classpath.
The VM will look inside the jar file for the org/javaguy/coolframework
part, and find your class.
So, classpaths contain:
JAR files, and Paths to the top of package hierarchies....
but if java only looks for classes in directories specified by CLASSPATH variable how does java find classes from libraries that are part of JRE?

JAR doesn't include root files

I have simple Java Application and trying to create JAR to distribute using eclipse.
But when I look inside JAR it doesn't contain the test.txt file. I created JAR as Export>Runnable JAR File

You need to put that file into one of your source folders (such as src). Only those get copied into the jar file (by default).

See the following image:
Choose the file which you want to add in jar file.

Netbeans Clean & build classes

When I clean and build a project in NetBeans, the .jar file appears in the dist folder, like it's supposed to. But what if I have multiple files under the project? What happens to those files? E.g. I have a Game project, and under it are the different characters(knight, rogue, etc.) but I only see a game.jar file when I clean and build, I want to know what happens to the individual files. Thanks

Those files should be in the jar file as compiled .class files. It's easy to double check what's in the jar file since it's in zip format. You can use a program like 7-Zip to open it, or rename it to the zip extension (e.g. from mygame.jar to mygame.zip) and whatever OS you're using probably has some way to open it.
When you open or extract the jar file you'll find the compiled class files in a directory structure that reflects your package structure. For example, if you have Knight.java in the directory src/game/characters/Knight.java in the jar file you'll find something like classes/game/characters/Knight.class.
The name "jar" is an abbreviation of "Java archive". It stores all the classes and other resources (for example, images) in a project.

The classes you have defined in .java files will be compiled into .class files - these are contained in the .jar file.

All resources get compiled into the JAR file. If you want a separate JAR for the resources, you'll need to split the project into two maven projects: one jar for the code, one for the resources. You can then create a third project that would generate a distribution.
That's a lot of work, though. It's.a lot easier tO keep everything in one JAR unless you have explicit dynamic loading requirements.

Updating .class file in jar

I want to update a .class file in a jar with a new one. What is the easiest way to do it, especially in the Eclipse IDE?

This tutorial details how to update a jar file
jar -uf jar-file <optional_folder_structure>/input-file(s)
where 'u' means update.

Do you want to do it automatically or manually? If manually, a JAR file is really just a ZIP file, so you should be able to open it with any ZIP reader. (You may need to change the extension first.) If you want to update the JAR file automatically via Eclipse, you may want to look into Ant support in Eclipse and look at the zip task.

Use jar -xvf to extract the files to a directory.
Make your changes and replace the classes.
Use jar -cvf to create a new jar file.

Simply drag and drop your new class file to the JAR using 7-Zip or Winzip. You can even modify a JAR file that is included in a WAR file using the parent folder icon, and click Ok when 7zip detects that the inside file has been modified

Jar is an archive, you can replace a file in it by yourself in your favourite file manager (Total Commander for example).

A JAR file is just a .zip in disguise. The zipped folder contains .class files.
If you're on macOS:
Rename the file to possess the '.zip' extension. e.g. myJar.jar -> myJar.zip.
Decompress the '.zip' (double click on it). A new folder called 'myJar' will appear
Find and replace the .class file with your new .class file.
Select all the contents of the folder 'myJar' and choose 'Compress x items'. DO NOT ZIP THE FOLDER ITSELF, ONLY ITS CONTENTS
Miscellaneous - Compiling a single .class file, with reference to a original jar, on macOS
Make a file myClass.java, containing your code.
Open terminal from Spotlight.
javac -classpath originalJar.jar myClass.java This will create your compiled class called myClass.class.
From here, follow the steps above. You can also use Eclipse to compile it, simply reference the original jar by right clicking on the project, 'Build Path' -> 'Add External Archives'. From here you should be able to compile it as a jar, and use the zip technique above to retrieve the class from the jar.

Editing properties/my_app.properties file inside jar:
"zip -u /var/opt/my-jar-with-dependencies.jar properties/my_app.properties". Basically "zip -u <source> <dest>", where dest is relative to the jar extract folder.

High-level steps:
Setup the environment
Use JD-GUI to peek into the JAR file
Unpack the JAR file
Modify the .class file with a Java Bytecode Editor
Update the modified classes into existing JAR file
Verify it with JD-GUI
Refer below link for detailed steps and methods to do it,
https://www.talksinfo.com/how-to-edit-class-file-from-a-jar/

1) you can extract the file into a folder called
jarname.jar
and then replace the file in the folder, handy if you are updating the class a lot while debugging
2) you can extract the jar replace the file then the jar it up again
3) Open the jar with 7 zip and drag and drop your new class in to copy over the old one

You can find source code of any .jar file online, import the same project in your IDE with basic setups. Make necessary changes in .java file and compile it for .class files.
Once compilation is done You need to extract the jar file, replace the old .class file with new one.
And use below command for reconstruct .jar file
Jar cf test.jar *
Note : I have done so many time this changes in our project, hope you will find it useful.

An alternative is not to replace the .class file in the jar file. Instead put it into a new jar file and ensure that it appears earlier on your classpath than the original jar file.
Not sure I would recommend this for production software but for development it is quick and easy.

Files not extracted from .jar file when run

I have updated my ant build.xml file to include a new file and a new folder. After creating the .jar I check if they exist in the jar by 'unzip\extract', and they are there.
But when executing the .jar neither the folder or the file gets extracted.
Am I missing a step?

Look into getResourceAsStream. It'll keep you from having to extract the files from the jar file. Unless that's your goal.

Your application should be able to use the file directly from within the jar, no need for extracting it. Or do you mean something else?

Are you doing something specific to extract the jar file? I ask because normally jar files are not extracted when executing them.
If you run "java -jar myJar.jar" or "java -cp myJar.jar com.example.MyMainClass" the jar files that is referenced will not be extracted. Java will load your classes and resources directly from the jar file without extracting it.

If you wrap your application up using One-JAR, you can specify an attribute in the Manifest file to extract files that you want (See the One-Jar-Expand manifest attribute).
As a bonus, you will also be able to wrap any dependent libraries along with your code, creating a single distributable jar.