Grails 4 bootRun lost build/resources/main/ classpath.

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### Task List

- [ ] Steps to reproduce provided
- [ ] Stacktrace (if present) provided
- [ ] Example that reproduces the problem uploaded to Github
- [ ] Full description of the issue provided (see below)

### Steps to Reproduce

Here is a sample `BootStrap.groovy`:

```groovy
class BootStrap {
def init = { servletContext ->
System.getProperties().get("java.class.path").split(File.pathSeparator).each {
println(it)
}
}
}
```

`./gradlew bootRun` or `./grailsw run-app` output:

```txt
/home/fengyu/projects/creative/grails-rest-seed/src/main/resources
/home/fengyu/projects/creative/grails-rest-seed/grails-app/views
/home/fengyu/projects/creative/grails-rest-seed/grails-app/i18n
/home/fengyu/projects/creative/grails-rest-seed/grails-app/conf
/home/fengyu/projects/creative/grails-rest-seed/grails-app/migrations
/home/fengyu/projects/creative/grails-rest-seed/build/classes/java/main
/home/fengyu/projects/creative/grails-rest-seed/build/classes/groovy/main
/home/fengyu/projects/creative/grails-rest-seed/build/gson-classes/main
/home/fengyu/.gradle/caches/modules-2/files-2.1/org.springframework.boot/ ...
...
```

Lost `build/resources/main` in classpath.

But `./gradlew check` or `./grailsw test-app` output:

```txt
/home/fengyu/projects/creative/grails-rest-seed/build/classes/java/integrationTest
/home/fengyu/projects/creative/grails-rest-seed/build/classes/groovy/integrationTest
/home/fengyu/projects/creative/grails-rest-seed/build/resources/integrationTest
/home/fengyu/projects/creative/grails-rest-seed/build/classes/java/main
/home/fengyu/projects/creative/grails-rest-seed/build/classes/groovy/main
/home/fengyu/projects/creative/grails-rest-seed/build/resources/main # <===== Here
/home/fengyu/projects/creative/grails-rest-seed/build/gson-classes/main
/home/fengyu/projects/creative/grails-rest-seed/build/classes/java/test
/home/fengyu/projects/creative/grails-rest-seed/build/classes/groovy/test
/home/fengyu/projects/creative/grails-rest-seed/build/resources/test
/home/fengyu/.gradle/caches/modules-2/files-2.1/org.springframework.boot/...
...
```

Contains `build/resources/main` in classpath

### Expected Behaviour

`bootRun` should contain `build/resources/main` classpath

### Actual Behaviour

Since Grails 4.0 lost `build/resources/main` classpath when bootRun

### Environment Information

- **Operating System**: Linux
- **Grails Version:** 4.0.5
- **JDK Version:** 1.8
- **Container Version (If Applicable):** TODO

Start by reproducing the classpath output with ./gradlew bootRun or ./grailsw run-app, then compare it with ./gradlew check or ./grailsw test-app. The change is done when bootRun includes build/resources/main in its classpath, matching the expected output.

Written by the indexing model from the issue text.