Adding "runtime" libraries in a Gradle build happens neither smoothly nor at all

>But note that their "scope" is "Compile" for some reason that is left unexplained. 

Compile - means at cimpile and runtime scopes, please see related documentation about dependencies scopes.

>Anyway, switching them to "runtime" and clicking "Apply" gives a cryptic warning at the bottom of the dialog, which I interprete to mean that, if I change the "build.gradle" file later, the changes in this dialog will be lost.

Yes. In a Gradle/maven - based projects, IDE takes all configuration related to building and project structure from build files. So any chnages in the UI to the project structure will be lost on re-import from Gradle/Maven.

>But it still doesn't work, alas:

Do you have Gradle or IntelliJ IDEA set for Settings (Preferences on macOS) | Build, Execution, Deployment | Build Tools | Gradle | Build and run using option?

How does it work if you run it by Gradle from the command line? If you get same error from command line Gradle, it is likely the issue with dependencies configuration. E.g. check that you are using only compatible versions: https://stackoverflow.com/a/69283301/2000323

Thank you Andrey!

I have tried to create a new project with the same content to isolate the problem - and found the error:

In the runtime configuration, the classpath argument was pointing to the project directory toplevel ("phasmomycin2") -- as shown below -- instead of the "main" java directory ("phasmomycin2.main"). (Those are placeholders resolved by IDEA, right?) I don't know how that happened.

Note that IDEA highlights the textarea with the "class to execute" in red because it can't find that class. However, running this erroneous configuration still works (although not if you need 3rd party libraries apparently).

I was thinking about fixing the highlighted textarea "later", well it's fixed now.

Additionally, to make doubly sure that everything is configured properly, I manually removed the jackson dependencies from build.gradle and re-added them as described in

https://www.jetbrains.com/help/idea/work-with-gradle-dependency-diagram.html - "Gradle dependencies" Last modified: 07 September 2021

Right Click in the window for build.gradle inside the "dependencies" block":  "Generate" > "Add Maven Artifact Dependency" then "Search for Artifact", which yields the expected text in build.gradle

implementation 'com.fasterxml.jackson.core:jackson-core:2.13.1'
implementation 'com.fasterxml.jackson.core:jackson-annotations:2.13.1'
implementation 'com.fasterxml.jackson.core:jackson-databind:2.13.1'
implementation 'com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.13.1'

The "Gradle Tool" (clickable element on the right border) then says:

Checking against File > Project Settings > Modules shows the dependencies under "$PROJECT/main" as "Compile" (no "Runtime" entries):

All fine.

I had a similar situation where I needed to have ‘org.apache.logging.log4j.core’ as a runtime library but when I issued my gradle ‘run’ command in Intellij Idea I got:

java.lang.ClassNotFoundException: org.apache.logging.log4j.Logger

 despite including it as a dependency in my build.gradle as 

implementation (group: 'org.apache.logging.log4j', name: 'log4j-core', version: '2.20.0')

In the end I fixed this by including requires org.apache.logging.log4j in my module-info.java:

module mymodule {
    exports mymodule; 

    // simple logging facade for compile time  
    requires org.slf4j;   

    // required log4j core for run time binding   
    requires org.apache.logging.log4j;  
}