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Java modules in IntelliJ and adding require java.ws.rs gives bizarre error

We have maven apps that until recently were on JDK8. We just upgraded them to JDK11 and are trying to take advantage of the JPMS from JDK9 by making our utility libraries into modules.
We originally had this kind of path:
utils/some-library1/src/main/java/com/company/team/utils/lib1/Util1.java
There, java is the "source root".
So a colleague placed the module-info.java file in the lib1 folder and declared it thus:
module utils.lib1 {
exports com.company.team.utils.lib1;
}
From the command line that builds and works, so he assumes everything is all module-y goodness.
But when I opened in Intellij, it had an ugly red line and the message said I should move it to source root. It then moved it to the "java" folder above. Fair enough.
That caused me to dig around trying to find out more about this JPMS that my colleague had implemented. After a lot of searching and experiments, I also determined that the "java" folder, as "source root", should be renamed to the name of the module ("utils.lib1"). So now I have these two files:
utils/some-library1/src/main/utils.lib1/module-info.java
utils/some-library1/src/main/utils.lib1/com/company/team/utils/lib1/Util1.java
And even Intellij is happy. Hooray! So I refactor all the other libraries. Suddenly I hit a major snag in let's call it lib2 with this line:
module utils.lib2 {
exports com.company.team.utils.lib2;
requires java.ws.rs;
}
Intellij flags the module with the red error squiggle again, this time saying:
Module 'utils.lib2' reads package 'javax.activation' from both 'jakarta.activation' and 'jakarta.activation'
I did some digging and found out the following:
java.ws.rs pulls in one of the following (it depends on which app):
javax.ws.rs-api-2.1.1.jar
jakarta.ws.rs-api-2.1.6.jar
Their module-info.java files contain this line:
requires transitive java.xml.bind;
Which pulls in one of:
jakarta.xml.bind-api-2.3.2.jar
jakarta.xml.bind-api-2.3.3.jar
jaxb-api-2.4.0-b180830.0359.jar
Which all have this line:
requires transitive jakarta.activation;
And that's where I give up. Our libraries are big hefty things that are hard to parse completely, so to simplify I created a maven app with just one class and all it does is import javax.ws.rs.core.Link.
And IntelliJ still gives that crazy error that I can't figure out and Google has been adamant in refusing to tell me.
Is it really broken or is Intellij just as confused as I?
I gave the long story both to show what we've done and to let you know that I'm very new to modules. So if it's a simple thing, please excuse me. I am just stumped though.
Additionally, are there any obvious tests one can perform at the command line to validate module configuration?
I've had inconsistent luck with jdeps, javac, and actually running as indicators of problems.
My suspicion is that things only work now because they're all in the unnamed module. But I need to get everything working if I'm going to convince anyone to change it.
EDIT
This question was reported as already answered, but that is incorrect. The suggested link deals with two different packages (A & B) importing package X. But in my case, the error is that the same package (A & A) imports package X. And this is done a few transitives down, so I have no control over the imports and can't see how to do an exclusion. Also, this problem can be repeated with just single requires statement in module-info.java!
Plus, there is a second question here that is also important that has not been addressed: how to validate the module configuration from command line (without involving the IDE at all).

I also determined that the "java" folder, as "source root", should be renamed to the name of the module
No, it should not. The java source root should be left as is but you must create a package name corresponding to your module name, so it should be /src/main/java/ - source root and then utils/lib1 directory - whidh would be the package.

I came across exact same warning in Intellij and it was genuine. In my case the collision was coming from three separate dependencies using same module name (i.e. 'jakarta.activation'):
'jakarta.activation:jakarta.activation-api:1.2.2'
'javax.activation:javax.activation-api:1.2.0'
'com.sun.activation:jakarta.activation:1.2.2'
It got it resolved for my project by applying explicit exclusions on dependencies which were pulling the last two.

Eclipse error: “The import ... cannot be resolved”

I know I am asking the very popular question. But I can not find the solution to the problem. I have a sandbox to which I added a code of the unit test MulticurveBuildingDiscountingDiscountAUDTest.java file and commented it.
Then I added the main method and I could successfully run the program (print something in a console).
Finally, I uncommented the code of the MulticurveBuildingDiscountingDiscountAUDTest.java file and I saw the following error:
The import com.opengamma.analytics.financial.instrument.index.GeneratorSwapFixedONMaster cannot be resolved.
And further in the code:
GeneratorSwapFixedONMaster cannot be resolved
I know that this import is located in the og-analytics src/test/java location, which I believe is not listed anywhere in the build path. I believe the problem is with a build path options and specially with classes like GeneratorSwapFixedONMaster which were created specially for tests. I have been playing around with cleaning, rebuilding projects, reinstalling and as a result updating the JRE. I have visited these Import *** cannot be resolved [duplicate] and these Eclipse error: “The import XXX cannot be resolved” questions.
Do you know what shall I do to cure the following error?
I have many problems with other imports from the original MulticurveBuildingDiscountingDiscountAUDTest.java file as well.
Update: #1 is a location of my file. #2 is the location of classes this project uses. The MulticurveBuildingDiscountingDiscountAUDTest.java file is taken from the src/test/java
Update 2: one may see that in Libraries I have included all the dependencies I might need (at least I do not know what else to add). The Maven Dependencies contains the hole og-analytics package:

You included the source (src) folder og-analytics/src/main/java which contains the *.java files instead of the classes (bin or classes) folder with the *.class files (in your case, probably og-analytics/target/classes).
But instead using Add Class Folder... you should add the project og-analytics in the tab Projects. Or even better, in the Maven pom.xml file add the dependency to the project og-analytics like you did for og-util.

I know that this import is located in the og-analytics src/test/java location, which I believe is not listed anywhere in the build path.
Perfectly explains your problem. In order to import any class, you must either have the source in your build path, or some directory that contains a compiled version of that class. It is that simply.
The answer is: get clear on your project setup. If you intend to use classes from somewhere, you have to make them available somehow. Otherwise it will not work. In your case: if your tests want to make use a certain thing - then you should probably add that "thing" to your test project (you should avoid putting test-only stuff to your "product" projects).
That is all there is to this.

Where does IntelliJ put .class files when it compiles during typing

Is IntelliJ compiling all the time since it tells me with red squiggly lines when there is an error? (in addition to the autocomplete features) Or is it doing some sort of psuedo compiling?
If it is doing legit compiling, where does it put these compiled classes? I'de like to point my JRebel to that directory instead of the individual module target folders.

Meo is right, from what I learned when I developed plugins for custom languages, IntelliJ does not compile anything until you explicitly make your project. While you are typing, its lexer/parser detects any invalid token or code construct. In the meantime, it maintains an index of every class and method in your project and its dependencies, along with their signature, etc.
After you stop typing, you'll see a little colored eye in the top part of the right gutter. It indicates that the IDE is running "annotators" and "code inspections". They are able to tell whether or not classes, methods and variable are valid based on the current index and the current state of your file (imports, declarations, etc.). The same goes for unused variables, invalid parameters in method calls, etc.
Pros:
annotators work directly on what they call a PSI tree, which is basically an enhanced AST representing your current file
it may be faster that compiling every time (it uses an index and does not need to recompile every dependent class)
annotators can detect things javac don't care about, such as potential bugs (e.g. using = instead of == in a while condition)
Cons:
that's a loooot of work, basically they need to rewrite the logic to find every error that javac can produce (which is why you can find many issues on their bugtracker labelled "good code is red" or "bad code is green", meaning there is a difference between what they detect and what the compiler would output)
TL;DR: it does not produce any .class until you make your project, everything is done "by hand"

For every module, the compiler output path can be found from Paths tab in Module Settings.
JRebel plugin generates rebel.xml automatically and derives the directory path from Module Settings, so you do not need to point to the locations manually - just generate rebel.xml using the IDE plugin: right click on module in the project view -> JRebel -> generate rebel.xml

Just to add, after compilation, the classes are stored in the target directory if it's a Maven project - otherwise, the directory is specified in IntelliJ's Project Structure, in "Project compiler output":

IntelliJ understands the code, it does not need to compile the code to know what is wrong.

I found my .class files by going to the out/production/main folders from the home directory of the project.

IntelliJ reports "sources not found" even though source opened in other module

I have
ScanResults results; // me.unroll.scanner.ScanResults
logFilterStateReceived(filterState, results.googleImage);
I just added the field googleImage. It's giving me the error "Cannot resolve symbol 'googleImage". When I jump to the declaration of ScanResults it fails to retrieve the source and recompiles something - something, I don't know what - into an obsolete version of my Scanner module.
So
the Scanner module is open
in Project Structure > Email-Lib, where the above code sample lives, Scanner is listed as a compile dependency with the little folder icon, which I think means it's working / on disc
I redeployed the code to Maven in any case.
Why is it not pulling the local code?

I had Scanner listed as a dependency twice. One was as a module and one was as a Maven jar. What probably happened is I loaded the higher library before the I added the lower one as a module, although I'm not sure why it preferred the module dependency (besides it being higher in the list). Removing the library dependency fixed it, although I would expect my build to break if I close the module. This is something Eclipse seemed better at handling automatically (prefer open project, fallback to Maven repo).

Compile-time created class is shown as non-existent in IntelliJ

Motivation:
I'd like to try if compile-time annotation processing fits my problem. It needs to work out of the box, no compiler arguments etc.
Current state:
I have:
The annotation
An annotation processor
A .jar containing both of these and a javax.annotation.processing.Processor file containing the FQCN of my processor in META-INF/services
What should happen:
It should autodetect the processor
It should process the annotation and create a new class (WiredAnnotated)
I should be able to use this class in one step of compilation (not multiple phases)
I wan't the editor to accept this class is generated (e.g. AndroidAnnotations manages this as well)
What actually happens:
It autodetects the processor
It creates a new class (in out/production/*/generated/)
I am able to use this class
The source code looks right
When decompiling it looks ok too
The editor cannot resolve the class (see screenshot)
What I tried:
Restarting IntelliJ
Invalidating caches
Checking for output of the annotation processor
Screenshot:
When compiling, it actually works as expected. I guess it has something to do with inspecting the wrong directories.
Does anyone have an idea/clue on what I'm doing wrong? Did I miss information which could help you help me?
Thanks in advance, Till

Well, you need to add you out/production/*/generated/ to projects source folder. So, IntelliJ will know about your generated classes.
You can make it via Right click on directory > Mark directory as source root.
or
Project structure (F4) > Modules > Sources tab > Source folders should contain all directories with your source codes, generated one inludes.
In android there is a gen dir in root folder, but notice, it glows blue or green which means it marked as Source folder, it is also visible in Project structure > Modules. It contains R, BuildConfig and Manifest.