Develop Reference

How to add a class on classpath in Intellij?

I have the following project structure in Intellij:
I am actually working with a maven project and all I wanna do is just run the project. Unfortunatelly I dont understand why but when I run the class called GenerateGraph it shows me the following error:
Error: Could not find or load main class graph.GenerateGraph
Caused by: java.lang.ClassNotFoundException: graph.GenerateGraph
I dont understand why this happens- it is the first time I encounter something like that. When I go on project structure I see the following:
Run configuration:
seems like it doesnt even see that the graph package has a class inside. Could someone maybe help me understand what has happened? Is it because I renamed the package after importing the project? Thank you very much in advance

Your project is not setup correctly.
You have reverseGraph marked as the sources root. In this case, src is the source folder.
The typical Maven project structure is src/main/java for non-test source files and src/test/java for tests.
What I'd recommend is modifying your folder structure:
Remove reverseGraph
Move src to the root of the project.
Add a src/main/java folder, and move your graph folder into that.
Reimport the Maven project in IntelliJ, and it should automatically flag the java folder in src/main as the sources root.

Most likely the dependencies are not correctly set up - because you do not have this project opened as Maven project in IDE. Please import this project as Maven project, see steps from Open an existing Maven project IntelliJ IDEA documentation section.

Can files outside of the Maven folder structure get compiled?

We have a Java project that was modified about 2 years ago based on the dates.
The project uses a the Play Framework which as I recalled built and ran just fine back in 2012.
The developer apparently had tried to change the project to be a Maven project but the folder structure is all over the place and not within the Maven src folder structure.
Attempting to run the Play commands does not work on building the project any longer and using the Maven commands does not compile the code.
What occurs is just the packaging of all of the folders and source code into a .jar file.
So the question is 'Can files outside of the Maven folder structure get compiled?' if so how, OR do I need to restructure all the code to be placed into the proper Maven folder structure to try and get this to work again?
Thanks for your time.
Rough view of the folder tree below: Unable to post the POM as it is on another system
Project Name
src
main/java/
trunk
Project Name
... play framework folder structure in here eclipse, modules, precompiled, tmp
conf
lib
Web Content
META-INF
WEB-INF

Yes you can compile files in a non-standard Maven folder structure. Maven natively supports multiple source directories for the purposes of generated sources.
Read the Maven use guide When You Can't Use the Conventions
Using Multiple Source Directories This occurs when you are producing a
single JAR (or other artifact), and have several source directories
with classes you want to include.
This answer shows how to edit the directory structure in Maven by specifying the appropriate properties to override from the superpom.
The Maven pom docs show the build element set mentioned in the link above.
As a side note this answer covers a non standard directory layout for building war.

Intellij idea specify output folder for each source folder (like in eclipse)

I'm working with huge project which has almost hundred plugins which in turn has it's own folder. The issue is that this project was created in eclipse and for each plugin's source folder a corresponding output folder specified. I'm wondering if it is possible to do the same thing in intellij or I'm forced to use eclipse?
Just some screenshots to make thigs clearer:

In the project structure you can create an artifact for each of your library an specify an output directory.
Try File->Project Structure then in the Project Setting add new artifact and specify output directory

"Could not find or load main class" after removing Maven nature and files (pom.xml, target/) from an Eclipse Project

I accidentally converted my project to Maven by going to Configure > Convert to Maven Project. Now I want to undo this. I read that I need to right click Maven > Disable Maven Nature and that worked fine. However I want to totally remove Maven, so I deleted the pom.xml and the target folder. When I try to run my code now, I get the error:
Error: Could not find or load main class
So what am I missing? How do I revert from a Maven project to a non-Maven project?

When you convert a Java project to a Maven project in Eclipse, the Maven Integration for Eclipse (m2eclipse) configures the Java incremental compiler to put the compiled class files in the same location as Maven would put them, i.e. target/classes.
So when you remove the Maven nature and delete the target folder, you now also have deleted the compiled class files and your project can no longer run. AFAIK, the incremental compiler doesn't detect when you remove its output files, so you need to trigger a rebuild by cleaning the project (Project > Clean...)
This will fix the problem that you can not launch your project, but may re-create a target folder. If you also want this to be "fixed", you can switch back to some other folder name for the binaries, e.g. bin, in the project's Java Build Path configuration on the Source tab.

Is it basically a Maven project, i.e., do you have and maintain it through a pom.xml? Then my suggestion is to delete the project in Eclipse but keep the files on the disk (i.e., it removes it from the workspace). Then, run a simple mvn eclipse:clean eclipse:eclipse which creates a simple Java project without the Maven nature based on the POM (so the libraries are linked and the source/output directories are set up correctly - this may solve your ClassNotFoundError).
If it's a simple Java project, I would advise deleting it from the workspace, removing the .classpath and .project files and importing it again with the Create a Java project with existing sources wizard.
Either way, make a backup of your project before you start doing anything :-)

How to prevent Eclipse from cleaning the bin folder for every build?

I am now doing a project using Eclipse, and I have some resource files (e.g., image, text) saved in the bin folder, and these files are needed by the program.
However, with every build, Eclipse would try to clean up the folder, then rebuild the project. When cleaning, it deletes the resource files in the folder. Is there anyway to stop Eclipse from doing this?
I know I could change the location of the files, but I am also curious why Eclipse would do this, and could this be prevented from happening.
Thanks!

Go to Options -> Java-> Compiler -> Building and uncheck Scrub output folders when cleaning projects.
That did the trick for me. In my project, I have an Ant task that adds a few configuration resources to the bin folder to include them in the classpath, without having them in src

I can't say exactly why it does it, but probably that's just how Eclipse does the build: empty the "output folder" and start compiling.
That said, if you put your files into a source folder, then Eclipse will simply copy the files over to bin on every build and they won't disappear. It will do this to any file it doesn't know how to compile, e.g. .xml, .xsd, .png, etc.

You can consider using a maven style project and add the resources to the resources folder.
Here is a link to maven directory layout.
What kind of project you are using in eclipse. You can turn off build automatically feature in the Project menu. Which would stop eclipse from cleaning up projects automatically.

Copy and paste your resources into the source folder. In eclipse, in package explorer, find your project, then paste into src. It then gives an option to copy the file or link to it. Click copy and it gets stored in /bin but won't get deleted.