fix(memory): strip extra properties from entities/relations to fix schema validation

[ctonneslan]

Problem

read_graph, search_nodes, and open_nodes fail with:

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

This happens when the memory.jsonl file contains entities with extra properties not defined in EntitySchema (e.g. custom_id, metadata from older versions, or properties added by external tools).

The MCP SDK validates structuredContent against the outputSchema and rejects entities with extra fields.

Fix

Strip entities and relations to only include schema-defined fields before returning in all three graph-returning tools:

const cleanEntities = graph.entities.map(({ name, entityType, observations }) => ({
  name, entityType, observations
}));
const cleanRelations = graph.relations.map(({ from, to, relationType }) => ({
  from, to, relationType
}));

This ensures the output matches the schema while preserving all data in the underlying JSONL file (extra properties are still stored, just not returned in the structured output).

Fixes #3144