tool_serializer and filter_response appear to have no effect on MCP client output

[ajorg]

Summary

The output_serializer function passed as tool_serializer to FastMCP() doesn't appear to transform the output that MCP clients actually receive. TOON serialization and filter_response() filtering (null removal, links stripping, items_active_record removal) are not reflected in what the client sees.

What I expected

With tool_serializer=output_serializer configured and OUTPUT_FORMAT=toon (the default), I expected MCP tool results to:

1. Have null/empty values stripped by remove_null_and_empty()
2. Have links keys removed
3. Have sensitive keys filtered by filter_sensitive_keys()
4. Be serialized in TOON format

What I observed

Tool results arrive at the MCP client as raw JSON dicts with no transformation applied — nulls, items_active_record, and all original fields are present. Tested with FastMCP 2.12.4 on Claude Code (Claude Desktop).

This suggests FastMCP may be returning structured_content (the raw dict) to the client and only applying tool_serializer to the content text representation, which the client ignores when structured content is available.

Impact

• filter_response() pipeline in utils.py is effectively dead code
• TOON output format configuration has no observable effect
• The python-toon dependency is unused in practice

Questions

1. Was tool_serializer intended to transform what MCP clients receive, or only the text fallback?
2. If the former, is this a FastMCP bug that should be raised upstream?
3. Should the filtering/serialization be restructured to work with how FastMCP actually delivers results?

Additional context

This was discovered while migrating to FastMCP 3.0, which removed tool_serializer entirely. A middleware-based replacement (OutputSerializerMiddleware) has the same limitation — structured_content bypasses the serialized text.

[ajorg]

I have a draft migration to FastMCP 3.0 using the middleware API on my fork: ajorg:fastmcp3-middleware. It replaces tool_serializer with an OutputSerializerMiddleware and the filtering works, but we're holding off because the same question applies — structured_content bypasses the TOON-serialized text, so we need to decide what to do with TOON output before moving forward with the migration.

In the meantime, #5 pins fastmcp to 2.x to prevent breakage.