fix(memory): skip duplicate entities and relations within a single batch

[JSap0914]

Description

create_entities and create_relations only de-duplicated against the existing graph, never against the items in the incoming request. So passing the same entity name (or an identical relation) twice in a single call persisted duplicate records to memory.jsonl.

This contradicts the documented behavior in the README — "Ignores entities with existing names" and "Skips duplicate relations" — and breaks the implicit name-uniqueness invariant the rest of the manager relies on (addObservations/deleteEntities/deleteObservations all key on name, and find() only returns the first match).

The fix de-duplicates within the input batch as well, keeping the first occurrence. Cross-call de-duplication is unchanged.

Server Details

• Server: memory
• Changes to: core logic (KnowledgeGraphManager.createEntities, KnowledgeGraphManager.createRelations)

Motivation and Context

Reproduction (before this change):

// create_entities
[{ "name": "Alice", "entityType": "person", "observations": ["a"] },
 { "name": "Alice", "entityType": "person", "observations": ["b"] }]
// -> graph now contains TWO "Alice" entities

// create_relations
[{ "from": "Alice", "to": "Bob", "relationType": "knows" },
 { "from": "Alice", "to": "Bob", "relationType": "knows" }]
// -> graph now contains TWO identical relations

After the change each of the above creates a single record, matching the documented "ignores existing names" / "skips duplicate relations" contract.

How Has This Been Tested?

Added two regression tests to src/memory/__tests__/knowledge-graph.test.ts (within-batch duplicate entities, within-batch duplicate relations) and ran the existing vitest suite:

$ npx vitest run            # in src/memory
 Test Files  2 passed (2)
      Tests  47 passed (47)

Both new tests fail on main (the manager returns/persists 2 records) and pass with this change. npx tsc --noEmit is clean.

Breaking Changes

None. Behavior only changes for inputs that were already malformed (duplicate items in one request); valid de-duplicating callers are unaffected.

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation update

Checklist

• I have read the MCP Protocol Documentation
• My changes follows MCP security best practices
• I have updated the server's README accordingly (no change needed — fix aligns behavior with the existing README description)
• I have tested this with an LLM client (verified via the vitest suite instead)
• My code follows the repository's style guidelines
• New and existing tests pass locally
• I have added appropriate error handling

Prepared with AI assistance; the diff, tests, and verification were reviewed by me.

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