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Move _AfterILLinkAdditionalSteps from the outer build into the inner (per-RID) build using AfterTargets="ILLink". This ensures AssemblyModifierPipeline runs on trimmed IL assemblies BEFORE CreateReadyToRunImages/IlcCompile compiles them to native code, preventing assembly modifications from overwriting R2R/AOT native code with pure IL. Add _CopySidecarXmlToAssemblyPaths target to copy .jlo.xml and .typemap.xml sidecar files from linked/ to wherever assemblies end up after R2R/AOT (e.g. R2R/, publish/), so outer-build consumers (_GenerateJavaStubs, GenerateTypeMappings) can find them. Handles: NativeAOT duplicate assemblies (KeepDuplicates="false"), R2R composite assemblies (empty sidecar files), assemblies not in ManagedAssemblyToLink (Touch AlwaysCreate), single-RID vs multi-RID path differences, and framework vs user assembly classification without NuGetPackageId (filter by known framework assembly names).
In NativeAOT builds, the project's own assembly is not in @(ManagedAssemblyToLink) — ILLink passes it as a TrimmerRootAssembly. This caused AssemblyModifierPipeline to skip it, producing no JCW for MainActivity and failing with XA0103. Add the root assembly explicitly to _AfterILLinkAssemblies using Exclude (not KeepDuplicates) to avoid duplicates. KeepDuplicates compares items including metadata, so a bare Include would be considered distinct from an existing item with rich metadata from @(ManagedAssemblyToLink), causing GetPerArchAssemblies() to throw a duplicate key error in CoreCLR builds. Exclude compares by ItemSpec only, correctly deduplicating in both scenarios. Also set HasMonoAndroidReference=true on the root assembly so IsAndroidAssembly() returns true and FindJavaObjectsStep scans it.
KeepDuplicates="false" compares items INCLUDING metadata, so when NativeAOT builds produce duplicate @(ManagedAssemblyToLink) entries for the same assembly (e.g. Java.Interop.dll) with different metadata, the transformed items survive deduplication and cause GetPerArchAssemblies() to throw "duplicate key" errors. Replace KeepDuplicates with the RemoveDuplicates task, which deduplicates by ItemSpec only, ignoring metadata differences.
… late When RuntimeIdentifier is set after path evaluation (e.g. via MockPrimaryCpuAbi.targets), IntermediateOutputPath does not contain the RID. The target now detects this and appends the RID explicitly to find sidecar XML files in the correct linked/ directory.
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Move _AfterILLinkAdditionalSteps from the outer build into the inner (per-RID) build using AfterTargets="ILLink". This ensures AssemblyModifierPipeline runs on trimmed IL assemblies BEFORE CreateReadyToRunImages/IlcCompile compiles them to native code, preventing assembly modifications from overwriting R2R/AOT native code with pure IL.
Add _CopySidecarXmlToAssemblyPaths target to copy .jlo.xml and .typemap.xml sidecar files from linked/ to wherever assemblies end up after R2R/AOT (e.g. R2R/, publish/), so outer-build consumers (_GenerateJavaStubs, GenerateTypeMappings) can find them.
Handles: NativeAOT duplicate assemblies (KeepDuplicates="false"), R2R composite assemblies (empty sidecar files), assemblies not in ManagedAssemblyToLink (Touch AlwaysCreate), single-RID vs multi-RID path differences, and framework vs user assembly classification without NuGetPackageId (filter by known framework assembly names).