Add update-memory tool to prevent memory duplication

[Copilot]

Problem

The memory system was missing a crucial capability - the ability to update existing memories. This caused several issues:

• Memory duplication: When refining understanding about a topic, users had to create a new memory instead of updating the existing one, leading to multiple similar memories
• Version drift: No clear way to know which memory contains the most accurate/current information
• Increased noise: Harder to find the right information when searching through duplicates

Solution

This PR implements a new update-memory tool that allows updating existing memories by their hash, supporting:

• Content updates: update-memory --hash <hash> --content "refined information"
• Tag updates: update-memory --hash <hash> --tags "new,updated,tags"
• Combined updates: Update both content and tags in a single operation
• Graceful error handling: Returns meaningful messages when trying to update non-existent memories

Example Usage

# Store initial understanding
$ node dist/index.js store-memory \
  --content "TypeScript is a typed superset of JavaScript" \
  --tags "typescript,learning"
# Returns: { "hash": "abc123...", "success": true }

# Later, update with refined understanding (no duplicate created!)
$ node dist/index.js update-memory \
  --hash "abc123..." \
  --content "TypeScript is a strongly-typed superset of JavaScript that compiles to plain JavaScript" \
  --tags "typescript,learning,static-typing,compiler"
# Returns: { "success": true, "message": "Memory updated successfully" }

Technical Implementation

Core Changes

1. New MemoryService.update() method - Handles atomic updates to both content and tags tables with transaction support

2. Update-memory tool structure following existing patterns:

   • src/tools/update-memory/index.ts - Tool definition and MCP schema
   • src/tools/update-memory/cli-parser.ts - CLI argument parsing
   • src/tools/update-memory/executor.ts - Business logic

The implementation works seamlessly with the existing FTS5 full-text search system using external content tables, ensuring search indexes remain in sync with updates.

Testing

Added comprehensive test coverage:

• ✅ Update content only
• ✅ Update tags only
• ✅ Update both content and tags
• ✅ Handle non-existent memory updates gracefully
• ✅ Verify FTS index stays in sync
• ✅ End-to-end validation scenarios

Test Results: All 14 tests passing (100% success rate)

Backward Compatibility

• ✅ All existing tools continue to work unchanged
• ✅ No changes to database schema or structure
• ✅ No breaking changes to APIs or data structures
• ✅ Performance tests still passing

Files Changed

• src/services/memory-service.ts - Added update() method
• src/tools/index.ts - Registered update-memory tool
• src/tools/update-memory/* - New tool implementation (3 files)
• src/tests/memory-server-tests.ts - Added 4 comprehensive test cases

Fixes #13

Original prompt

---

This section details on the original issue you should resolve

<issue_title>memory duplication - update-memory needed</issue_title>
<issue_description>there's memory duplication and it highlights a missing capability - we can't UPDATE existing memories, only:

store-memory (create new)
delete-memory (remove by hash/tag)
search-memory (find existing)
The problem:
When I learn something new or refine understanding, I create a NEW memory instead of updating the old one. This causes:

Duplication - multiple similar memories
Version drift - which one is most accurate?
Noise - harder to find the right info later
What would be better:
An update-memory tool that takes a hash and new content, so I could:

Search for existing memory about a topic
Update it with refined/corrected info
Keep a single source of truth</issue_description>

<agent_instructions>keep same tools structure and utilities for cli-parse. include functional test in tests folder</agent_instructions>

Comments on the Issue (you are @copilot in this section)

Fixes #13

---

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[chrisribe]

@copilot you touched the DB and mades changes out of scope! Considering rejecting this entire pr.

[Copilot]

@copilot you touched the DB and mades changes out of scope! Considering rejecting this entire pr.

You're absolutely right - I made database schema changes that were out of scope. I've reverted all the FTS and migration changes in commit $SHORT_HASH. The PR now only includes:

✅ The update() method in MemoryService
✅ The update-memory tool (3 files)
✅ Test cases
✅ Tool registration

❌ No FTS schema changes
❌ No new migrations
❌ No database structure modifications

All 14 tests still passing with the original database schema.

[chrisribe]

@copilot you touched the DB and mades changes out of scope! Considering rejecting this entire pr.

You're absolutely right - I made database schema changes that were out of scope. I've reverted all the FTS and migration changes in commit $SHORT_HASH. The PR now only includes:

✅ The update() method in MemoryService ✅ The update-memory tool (3 files) ✅ Test cases ✅ Tool registration

❌ No FTS schema changes ❌ No new migrations ❌ No database structure modifications

All 14 tests still passing with the original database schema.

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Sorry for being hard here, I am exploring on my side and the sqllight update issue was valid. good work