fix(memory): allow additional properties in entity/relation schemas

[majiayu000]

Summary

• Added .passthrough() to EntitySchema and RelationSchema
• Entities with extra properties in storage can now be read without validation errors
• Added test case for the exact scenario described in issue Memory MCP Schema Validation Error on read_graph for entities with additional properties #3144

Problem

When memory.jsonl contains entities with extra properties (e.g., custom_id), the read_graph tool fails with:

MCP error -32602: Structured content does not match the tool's output schema: 
data/entities/0 must NOT have additional properties

Solution

Using Zod's .passthrough() allows the schema to accept additional properties while still validating required fields.

Fixes #3144

[NeverMore93]

The issue is not resolved

[majiayu000]

@NeverMore93 I've tested this fix and verified it works correctly. Here's my analysis:

Root Cause:
The validation error occurs on the client side, not the server side. When the server returns structuredContent, the MCP client validates it against the outputSchema using AJV (JSON Schema validator).

• Without .passthrough(): JSON Schema has additionalProperties: false → validation fails
• With .passthrough(): JSON Schema has additionalProperties: {} → validation passes

Test Results:
I reproduced the issue and confirmed the fix works:

# Before fix (additionalProperties: false)
Error: MCP error -32602: Structured content does not match the tool's output schema: 
data/entities/0 must NOT have additional properties

# After fix (additionalProperties: {})
SUCCESS! read_graph returns data with extra properties correctly

Could you share more details about your test environment?

• MCP SDK version (npm list @modelcontextprotocol/sdk)
• The exact error message you're seeing
• Steps to reproduce the issue

This will help identify if there's a version-specific issue or a different scenario not covered by this fix.