KSP missing generated sources after Gradle incremental compilation

For details see https://github.com/google/dagger/issues/4878 and the repro example:

https://github.com/sam-step/dagger-ksp-incremental-repro

To make it easier to see the dependency tree I'll put it below:

If we do a clean build, everything builds fine. If we then trigger an incremental build by modifying only `OtherClass.kt` we get the following error:

```
> Task :app:kspKotlin FAILED
e: [ksp] ComponentProcessingStep was unable to process 'app.MyComponent' because 'generated.Generated_AnnotatedClassModule' could not be resolved.
```

The log files comparing the clean build to the incremental change are shown below.

**Note:** there's no `kspSourceToOutputs.log` entry for "`Build 1753820315477`"

### kspDirtySet.log

```
=== Build 1753820260259 ===
All Files
src/main/kotlin/app/App.kt
src/main/kotlin/app/AnnotatedClass.kt
src/main/kotlin/app/OtherClass.kt
src/main/kotlin/app/MyComponent.kt
src/main/kotlin/app/TargetAnnotation.kt
src/main/kotlin/app/ClassProvidedByGeneratedModule.kt
Modified
Removed
Disappeared Outputs
Affected By CP
Affected By new syms
Affected By sealed
CP changes
Dirty:
src/main/kotlin/app/App.kt
src/main/kotlin/app/AnnotatedClass.kt
src/main/kotlin/app/OtherClass.kt
src/main/kotlin/app/MyComponent.kt
src/main/kotlin/app/TargetAnnotation.kt
src/main/kotlin/app/ClassProvidedByGeneratedModule.kt

Dirty / All: 100.00%

=== Build 1753820315477 ===
All Files
src/main/kotlin/app/App.kt
src/main/kotlin/app/AnnotatedClass.kt
src/main/kotlin/app/OtherClass.kt
src/main/kotlin/app/MyComponent.kt
src/main/kotlin/app/TargetAnnotation.kt
src/main/kotlin/app/ClassProvidedByGeneratedModule.kt
Modified
src/main/kotlin/app/OtherClass.kt
Removed
Disappeared Outputs
Affected By CP
Affected By new syms
src/main/kotlin/app/MyComponent.kt
Affected By sealed
CP changes
Dirty:
src/main/kotlin/app/OtherClass.kt
src/main/kotlin/app/MyComponent.kt

Dirty / All: 33.33%
```

### kspSourceToOutputs.log

```
=== Build 1753820260259 ===
Accumulated source to outputs map
:
src/main/kotlin/app/AnnotatedClass.kt:
build/generated/ksp/main/kotlin/app/generated/Generated_AnnotatedClassModule.kt
src/main/kotlin/app/OtherClass.kt:
build/generated/ksp/main/java/app/OtherClass_Factory.java
build/generated/ksp/main/kotlin/app/generated/Generated_AnnotatedClassModule.kt:
build/generated/ksp/main/java/app/generated/Generated_AnnotatedClassModule_ProvideFactory.java
src/main/kotlin/app/MyComponent.kt:
build/generated/ksp/main/java/app/DaggerMyComponent.java

Reprocessed sources and their outputs
src/main/kotlin/app/AnnotatedClass.kt:
build/generated/ksp/main/kotlin/app/generated/Generated_AnnotatedClassModule.kt
src/main/kotlin/app/OtherClass.kt:
build/generated/ksp/main/java/app/OtherClass_Factory.java
build/generated/ksp/main/kotlin/app/generated/Generated_AnnotatedClassModule.kt:
build/generated/ksp/main/java/app/generated/Generated_AnnotatedClassModule_ProvideFactory.java
src/main/kotlin/app/MyComponent.kt:
build/generated/ksp/main/java/app/DaggerMyComponent.java

All reprocessed outputs
build/generated/ksp/main/kotlin/app/generated/Generated_AnnotatedClassModule.kt
build/generated/ksp/main/java/app/OtherClass_Factory.java
build/generated/ksp/main/java/app/generated/Generated_AnnotatedClassModule_ProvideFactory.java
build/generated/ksp/main/java/app/DaggerMyComponent.java
```

From the error message and logs it seems like the `Generated_AnnotatedClassModule` output was cleared/removed, but that seems wrong since `AnnotatedClass` isn't dirty and isn't reprocessed by the incremental change.

Start with the linked repro repository and compare the clean and incremental runs using kspDirtySet.log and kspSourceToOutputs.log. Read the related google/dagger#4878 issue and trace how the generated Generated_AnnotatedClassModule output is handled when only OtherClass.kt changes. Done means the incremental build retains or correctly regenerates that output and the app:kspKotlin task succeeds.

Written by the indexing model from the issue text.