We Keep Coding

Decompile JAR, Modify it, Recompile again?

I have an older Jar file which I have to modify in order to get it to work.
I have already decompiled it with jd-gui and changed the parts that needed change. I would now like to know what I have to do in order to get a jar back?
I guess that I have to add the libraries, but there is no extra lib directory.
How do I put everything together?
#Stephen C
"Therefore, when you make your changes and recompile, the resulting ".class" file could have unexpected "
How exactly is this relevant? I only want the function of the Jar file and not a 1:1 copy of it.
The Jar file is unsigned. What exactly would be the reason to sign a Jar file anyway? If I start it from another program?

If you are missing dependencies after decompiling the entire jar, that could mean the jar did not include them. When you create a jar, you can choose not to include dependencies in it, but this assumes that they will be available on the classpath at runtime. Check if there are any relationships with other jar files on the classpath when you run the original jar. See this answer for details on how to achieve this. Once you have identified all the dependencies, you can easily compile the jar from an IDE such as IntelliJ/Eclipse or from command line.
As a side note, if the changes you would like to make to the jar are minor or isolated I recommend editing the bytecode (much easier for small edits). I prefer this bytecode editor.
If decompilation fails on some parts of the code, the functionality of the jar will not be restored upon recompilation. In this case, instead of going through all available decompilers and hoping that you can decompile that code, I suggest you identify the set of classes which you are trying to edit, modify the rest of the classes such that they compile and do not have any side effects on the classes which are of interest to you (do not delete anything that is referenced by these) and compile the jar (even if this isn't the jar you want). You can then extract only the class files which you wanted to modify from the jar, and overwrite them in the original jar. This will only work if your changes didn't have any side effects.

If you are asking how to create a JAR:
You can do it using a build tool such as Maven, Gradle, Ant and so on.
You can do it using a Java IDE
You can do it using the command line jar tool; see How to create a JAR file from the official Oracle Java tutorials.
But it there is no guarantee that what you are doing will actually work. Here are a couple of the problems.
If the original JAR file was signed, you won't be able to re-sign the new JAR ... unless you have the private key that was used when signing.
Decompilation is often inaccurate. There is no guarantee that the Java code that it produces is a correct representation of the original class. Therefore, when you make your changes and recompile, the resulting ".class" file could have unexpected / unwanted differences relative to the original.
I guess that I have to add the libraries, but there is no extra lib directory.
I'm not sure what you mean by that. The (new) dependencies of the JAR don't necessarily need to be in the JAR itself. It depends on what kind of JAR it is; e.g. is it a so-called "executable" JAR that you launch using java -jar my.jar ....

Use jar plugins for gradle or maven for example, or build it with intelliJ, here's an answer in another post: How to build jars from IntelliJ properly?

Since I had trouble getting the .jar file completely recompiled and working with my application, I wanted to share here the steps that were missing in the previous answers.
In my specific case, to make things as easy as possible, I wanted to only modify one .java file in the result of the decompilation and update it directly in the .jar file.
I started from the answer from Paulo Ebermann on a similar question, and I ended up with:
javac -source 8 -target 8 -d classdir -cp \
"\
path/to/dep1.jar; \
path/to/dep2.jar; \
path/to/myoriginal.jar \
" path/to/my/java/class.java
cd classdir
jar -uf path/to/myoriginal.jar path/to/my/java/class.class
Notes:
the path/to/myoriginal.jar which is in the path of the dependencies, this forces the java compiler to look for missing classses in the original .jar file rather than in the local decompiled code (which would require recompilation and more dependencies) and therefore I have intentionally left out the . path in the list of class paths
the -source 8 -target 8 which were required to force the class to compile for the appropriate version of the runtime machine.
the -uf which indicates that the jar tool should only update the file with the provided class

Why don't I see code when viewing included Jar libraries in Eclipse?

There doesn't seem to be any code there. I expected to see class declarations so I could see what the code does but instead there's some
Are they somehow precompiled? What's the difference between included Jar file and a pure code?

You are looking at .class file, which is a generated when you compile .java file. To see what the program does, you have to look into .java file. You can refer official java documentation for that.
A .jar file is packaged file with .jar extension, it contains compiled java files and their class files. This file is usually imported into projects to use the classes defined in that package.
You can use "jar xf jar-file" command in command-prompt/terminal to extract the files from jar and look into the package.

A JAR will normally contain compiled class files. It may also contain source files or there may be a separate JAR that contains the source files, but not necessarily so.
If you want to use the library in your project, then a JAR of compiled class files is what you want. If you want the source code, then you'll have to see if it is available from wherever you downloaded this from. If all you want is to see how to use the classes, then probably what you want are JavaDocs for the library you are using. This is an HTML based API documentation.

Well, this is because you haven't attached any source for the mentioned dnsns.jar. You can attach source to existing JAR files in Eclipse. Refer this SO post: Is there an easy way to attach source in Eclipse?
For this specific dnsns.jar, it is part of your JRE, and if you are not able to see its source in your IDE, then it means that the Java that you have setup in IDE lacks the source. If your installation does not have the source (src.zip), then you can get it manually as mentioned on this SO post: Where to find Java JDK Source Code?
EDIT: Alternatively, you can also use a decompiler (e.g. http://jd.benow.ca/) to reverse engineer the source from byte code, though, it may not be the exact match to the original source but you can understand the overall idea. You can add the decompiler as the default program for opening .class files in eclipse Windows > Preferences > General > Editors > File Associations. Select *.class filter and add your decompiler as the program. Though, it is not as clean as attaching the source to JAR, but may work if you don't have access to source.
EDIT2: About your question
What's the difference between included Jar file and a pure code
Eclipse can find .java files for your own code because obviously they are in your workspace. But when you add a JAR file as library, it may have the source (.java) in it or not. If the source is available, eclipse can display it by default. If not, you have to add it manually.

How to update rt.jar file?

I want to add some class files to rt.jar. How am I able to do that?

Your question indicates you have some misunderstanding of the java platform.
First of all you need to know what the rt.jar is and what it does:
rt.jar is the jar that contains all the classes necessary for the java runtime. Hence it's name rt.jar
Now that you know that, you need to know how your java program runs:
Your java program, all your jars and classes are executed by the java virtual machine.
So as you can see the code you write & the rt.jar which is used by the java run time are completely separate and should remain so.
If you need some functionality you should add it to your jar.

Do not update it. Why do you want to update it?
Well anyhow if you want to update it, I know one way, You can open jar file in winrar and paste updated .class files in archive. But your jar may get in inconsistent state. Do it at your own risk.

You can use this command:
jar uf jar-file input-file(s)
Refer the link for details:
java.sun.com/docs/books/tutorial/deployment/jar/update.html

The best way to update the rt.jar is to install a newer version for Java. ;)
If you want to add your own classes in new packages, you can add these to a jar which is in your class path. This is preferable to changing existing classes.
If the only option is to change existing classes, you can create a "patch" in a jar which you prepend to your boot class path, or you can add the jar to an lib/endorsed directory. I wouldn't do this for production code, only for your own testing.

I've tried jar.exe with the u and 0 (i.e. zero) options and that gets the closest to looking like the original rt.jar file but if I've updated the JDK's JRE's rt.jar I have problems with compiling and jarring after the update. No idea why! Simply running a program with the JRE seems to work.
I also tried -Xbootclasspath/p but couldn't get it to work.
Looking at Replace a class within the Java class library with a custom version I see that there are legal problems with distributing an altered rt.jar to your customers, even if you could figure out how to do it correctly. So I plan to take the advice in that page and create a java agent. That's apparently legal and works.
One reason a person might want to modify rt.jar is to add debugging information after compiling the source that comes with the JDK with the -g option. One may also want to patch something. These would be for one's own use, of course.

Cleaning up stale .class files using Apache Ant

How do I clean up stale .class files out of ${workdir} given set of existing .java files in ${srcdir}? By stale I mean .class files that were generated from now removed .java files. I have tried coming up with something using Ant mappers and filesets etc. but I failed. Removing all .class files older than their respective source .java files would be acceptable, too.

I'm pretty sure there's an ant task to kill .classes older than the .java...
Depend sounds close, and may actually do what you want, but this isn't its intended purpose. Given developmentalinsanity's answer however, this may be the only thing that will Actually Work.

The problem is determining whether a class file without an obviously corresponding source file is really stale.
Try this in a single file (A.java)
public class A{}
class B{}
This will result in both A.class and B.class. So, B.class would seem stale because of the missing java file. You'd probably get similar issues with any inner classes.
Safest bet if you want to make sure there's no old class files lying around would be just to delete them all.

As it’s just not possible to detect what’s stale and what’s not, most builds have a clean target (that’s also part of cleanbuild). The clean target, just removes all files from you’re build directory. This directory normally is unversioned (svn:ignore).
Not all files in you’re build will be the result of the compiler, for example .property files, these files can be stored in an alternative directory that will be copies in to the build directory. For example in a web application build you can store those files in /web/WEB-INF/classes and let Ant copy them into the build directory.

Problems importing WAR files in Eclipse?

I was unfortunately forced to result to uploading a WAR file as my backup for a web application I am working on.
Luckily I have the most recent WAR file available. I am using Eclipse IDE and am using the Web Tools plugin for all the J2EE work that I am doing with the Dynamic Web Application Project.
When I imported my WAR file, and ran it on a local server, everything works fine. The problem I a ran into is that in the Java Resources/src folder that all my packages and .java files were now only consists of all the same packages, but they are empty.
I checked to see if I could find the files and I found the .class files in an "Imported files" folder that is not accessible in the Eclipse Project Explorer. I believe that I need to do some type of build or something so that my .java files are available for me, but unfortunately this is one area where I lack.
One thing I would also like to know is, one way or the other, am I able to obtain the .java source code files if I have access to the .class files?
Also, I would like to configure this environment as it was before where my Java Resources:src folder contaiend the packages and .java files.

One thing I would also like to know is, one way or the other, am I able to obtain the .java source code files if I have access to the .class files?
The short answer is No. There is no way to regenerate original source files from bytecode files.
If you were really, really desperate you could try to use a Java bytecode decompiler on your bytecode files, but the result will be be nothing like your original source code.
All comments and javadocs will be gone.
All original code layout will be gone.
Original local variable and parameter names may be gone, depending on your original compiler switches.
Constant expressions may have been pre-evaluated, and loops, string concatenations and other constructs may have been transformed unrecognizably.
Depending on the maturity of the decompiler, the Java code might not be semantically equivalent to the original code, and might not even be compilable.
I hope you haven't spent too long developing this application because the best answer may be to start again.