Develop Reference

Usage of jar with .java files and odd behavior of the compiler

I was curious about the differences between .jar with .class files and .jar with .java files. I partially got the answer here, But then what is the usefulness of .java files in the jar?
My guess is that the java files in the jar are like an interface that prevents compilation error, because I solved the IllegalAccessError thrown on runtime by replacing jar files with .class with jar files with .java specifically when using Xposed Framework. (Got the hint from this thread.)
Also
Thank you for your explanations and they were helpful. But I want to learn more about the differences in compiler's view, because I am wondering why my app works fine even if I only included the jar with java files, not class files (zxing). Also there are some cases that throws IllegalAccessException when I include the jar with class files, but not thrown when I include the jar with java files(xposed), even though I have to include at least one of them to make the compiler(AIDE) not complain about references, like unknown package. Why does the compiler not complain when I include only jar with java files though the compiler would not be able to resolve the actual implementation of the referred classes?

A .jar file is basically just a .zip file with another extension.
A .jar file with .class files have a special purpose and may have special meta-data (e.g. in META-INF folder).
A .jar file .java files is just a .zip file.
It is however common for open-source libraries to provide 3 .jar files:
One with .class files, to be used by your code, both to compile and to run your code.
One with .java files, to be used by your IDE, so you can drill into the library code and see it. Especially useful when stepping through the code with a debugger.
One with javadoc files (.html files), to be used by your IDE, so you can read the documentation about the classes and methods in the library. You do read the documentation, right?
None of those 3 files have to be named .jar. They could be renamed .zip so you could easily open them in your favorite Zip utility, or they could be renamed .foo just because...
They should be named .jar, to clarify that they are Java ARchives.

Its simple - *.java files are sources, *.class files are compiled classes.
What is used on runtime by JVM?? *.class files. Why would you put source files inside library? IDK, usally sources are distributed as separate jar, but all in all it is done to allow you to check library code without decompilation.

Cannot open java programs I saved in eclipse

I had no problem running my java code in eclipse last week and I have no problem creating a new java application in eclipse. However, I am unable to open any of the java program files in eclipse that I saved. I checked to see if my jdk se development kit was removed from my computer by mistake and it is still there. What do you think is wrong? Why can't I open my old files? All of my java programs are saved as CLASS files.

Source files are normally saved with a .java extension. Once you compile your source files, javac will generate you some files with a .class extension. These are not source files, and are usually deleted and recreated every time you compile your code. If you want to find your source code, you'll need to look for the .java files on your disk.
If you've deleted your .java files by accident, it is usually possible to decompile the class files into something resembling the original source, but much of the original formatting will be lost - comments etc. This approach is far from ideal, but may help you recover the situation if you cannot recover the original source files. A good decompiler can be found at http://jd.benow.ca/ - you can either download the standalone application, or it has plugins for Eclipse and IntelliJ.

Hi once you compile the source java files .java extn the class files will be created. Check your workspace in your disk there will be a folder as package as you created in eclipse under src folder.

Decompile Java Application packed with launch4j

I have a Java application that was converted to an .exe with launch4j. For several reasons I need to get access to the class files of the application.
The first thing I tried was unpacking the exe with 7zip. That way I get a handful of class files, but definately not the whole application packed in the exe (the class files seem to belong to launch4j).
What other options are there?

You can use something like this to extract the JAR from the Launch4j executable:
http://www.nirsoft.net/utils/resources_extract.html
Typically the executable packages necessary JAR's as executable resources and then looks for a JDK on the path to execute.
Once you get the JAR file you should be able to decompile it.

You cannot get access to class files. Exes are created, So that nobody can get access to your code.
If somehow , you are able to get access to jar files then you can decompile them to get the code and make changes.

Modifying a jar file

I have a jar file which is used in html file as applet. I want to modify the content of the jar file and to rebuild the jar file so that the html will work fine with the new jar file. How can i do this??
I already tried unzipping using 7zip nad modified the source and created the new jar. But when i use it in html it shows some java.lang.Classnotfound error

You can unjar or rejar the classes and source files as you wish.
unjar
jar -xvf abc.jar
jar
jar cf abc.jar input-files
http://docs.oracle.com/javase/tutorial/deployment/jar/build.html

Make the changes in the code (.java files), recompile to get the .class files. Then simply replace the old .class files in the jar with the new ones. I usually use WinZip, but you can use whatever app that can handle .Zip files. It should just work.
I've faced cases where the launcher of the app uses some sort of verification and checks for this kind of changes. I had to use a new launch script. This doesn't seem to be your case though.

This is surely possible from the command line. Use the u option for jar
From the Java Tutorials:
jar uf jar-file input-file(s)
"Any files already in the archive having the same pathname as a file being added will be overwritten."
See Updating a JAR File
A brief test shows this quickly updates changes apart from trying to delete the file.
I haven't seen this answer on other threads about modifying jar files, and many, marked as duplicates, suggest there is no alternative but to remake the jar completely. Please correct if wrong.

JARs are just ZIP files, use whatever utility you like and edit away!

Disclaimer: When reverse engineering any code be sure that you are staying within the limits of the law and adhering to the license of that code.
Follow the instructions above to unpack the JAR.
Find the original source of the JAR (perhaps its on SourceForge) and download the source, modify the source, and rebuild your own JAR.
You can also decompile the class files in the JAR. This is a rather advanced process and has a lot of "gotchas".

Call Scala code from Java?

I'm using Netbeans to write Scala and Java.
Netbeans generated a .jar file for the Scala project. I tried importing that file in the Java project. But I couldn't import any class from that .jar file into my Java project.
I also tried importing scala-library.jar to the java project, and could import classes from that jar.
I want to write my library in Scala, then expose a small interface that only involves Java stuff, then write a Java wrapper so that people can use it as a Java package. Is that possible? How do I do it?
Thank you very much.

There should be no problem in doing this.
Have you verified (e.g. using WinZip or the jar utility) that your .jar file actually contains the relevant .class files? (use jar tvf mylib.jar to check)
If you have verified that the correct .class files exist in your jar file, what is the runtime error you are seeing? Is it a NoClassDefFoundError? If so, which class cannot be found? How are you referring to the (Scala) class in your (Java) code?