Fix $ref pointer resolution after output schema wrapping

[weinong]

Summary

• Fix: After CreateOutputSchema() wraps a non-object schema under properties.result, rewrite all internal $ref JSON Pointers so they remain valid at their new location.
• Test: Add StructuredOutput_WithDuplicateTypeRefs_RewritesRefPointers to verify the fix.

Problem

System.Text.Json's JsonSchemaExporter deduplicates repeated types by emitting $ref pointers with absolute JSON Pointer paths (e.g., #/items/properties/foo/items). When CreateOutputSchema() wraps a non-object schema inside { "type": "object", "properties": { "result": <original> } }, these $ref paths become unresolvable because the original schema has moved under #/properties/result.

This breaks all tools that:

1. Return a non-object type (IEnumerable<T>, List<T>, arrays, primitives)
2. Have UseStructuredContent = true
3. Have a return type graph containing the same type at multiple locations (triggering $ref deduplication)

When a client calls tools/list, the broken schema causes JSON Schema validation errors. In MCP clients that don't isolate per-tool errors (e.g., the TypeScript SDK's cacheToolMetadata()), one broken tool schema prevents all tools from being enumerated.

Fix

Add RewriteRefPointers() — a recursive walk over the wrapped JSON tree that prepends /properties/result to every $ref value starting with #/. Called immediately after the wrapping block in CreateOutputSchema().

Reproduction

A minimal repro is available as a gist: https://gist.github.com/weinong/7a750e9b99c846dadc4fa41fc6c856fc

Fixes #1434

[Copilot]

Pull request overview

Fixes structured output JSON Schema generation for tools that return non-object types by ensuring $ref JSON Pointers remain valid after the schema is wrapped under properties.result (addresses #1434).

Changes:

• Add RewriteRefPointers to rewrite internal $ref values (#/… and #) after non-object output schemas are wrapped under properties.result.
• Add tests that validate wrapped structured output schemas still validate and that all $ref pointers resolve.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 1 comment.

File	Description
src/ModelContextProtocol.Core/Server/AIFunctionMcpServerTool.cs	Rewrites $ref JSON Pointer paths after wrapping non-object output schemas under properties.result.
tests/ModelContextProtocol.Tests/Server/McpServerToolTests.cs	Adds coverage for duplicated-type and recursive-type $ref scenarios to ensure rewritten pointers are resolvable post-wrapping.

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[eiriktsarpalis]

@stephentoub unless my knowledge of the stack is completely out of date, the encoding of method parameters as object properties happens at the AIFunctionFactory layer in Microsoft.Extensions.AI. Correspondingly, shouldn't this fix be applied in that library?

[eiriktsarpalis]

Nevermind, I just realized this specifically applies to the transform happening literally a few lines above. I'm assuming we already do apply the same fixup in corresponding AIFunctionFactory locations?

[eiriktsarpalis]

Why does the JsonObject require snapshotting while JsonArray does not? To my knowledge, both should allocate enumerators.