[Bug]: onnxruntime-node and sqlite-vec native modules also fail in Cowork sandbox (same root cause as better-sqlite3)

[kevintseng]

Component

MCP Server

Bug Description

In addition to better-sqlite3 (#73), two other native C++ dependencies are also blocked in the Claude Desktop Cowork sandbox:

Package	Version	Type	Impact
onnxruntime-node	^1.23.2	C++ addon (NAPI)	Embeddings system unavailable — semantic search, similar memory lookup, and all vector-based features fail
sqlite-vec	^0.1.7-alpha.2	C extension (SQLite loadable)	Vector search unavailable — sqlite-vec requires loading a native .so/.dylib extension into SQLite

Root cause is identical to #73: the Cowork sandbox has a read-only plugin filesystem and blocks node-gyp from downloading Node.js headers (HTTP 403 to nodejs.org).

Expected: All plugin features including embeddings and vector search should work in Cowork.
Actual: These features silently fail because the native modules cannot be compiled or loaded.

Steps to Reproduce

1. Install @pcircle/memesh plugin in Claude Desktop Cowork mode
2. Start a new Cowork session
3. Check if onnxruntime-node is loadable: node -e "require('onnxruntime-node')"
4. Check if sqlite-vec is loadable: node -e "require('sqlite-vec')"
5. Both fail with native module errors — no prebuilt binaries available and node-gyp compilation is blocked

Error for onnxruntime-node:

Error: Cannot find module '../../bin/napi-v3/linux/arm64/onnxruntime_binding.node'

Error for sqlite-vec:

Error: Cannot find module '../build/Release/sqlite_vec.node'

Error Output

For onnxruntime-node:
  Error: Cannot find module '../../bin/napi-v3/linux/arm64/onnxruntime_binding.node'
  - No prebuilt binary for linux-arm64 included in the package
  - node-gyp cannot compile: HTTP 403 downloading https://nodejs.org/download/release/v22.22.0/node-v22.22.0-headers.tar.gz

For sqlite-vec:
  Error: Cannot find module '../build/Release/sqlite_vec.node'
  - Same root cause: no prebuilt binary, node-gyp compilation blocked

Both failures trace back to:
  1. Read-only plugin filesystem (.claude-plugin/memesh/) prevents npm install
  2. Sandbox network restrictions block node-gyp header downloads (HTTP 403)

MeMesh Version

2.8.10

Claude Code Client

Other

Node.js Version

v22.22.0

Operating System

Linux

MCP Configuration

Additional Context

Environment:

• Client: Claude Desktop (Cowork mode) — selected "Other" as Cowork is not yet an option (see [Feature]: Add Claude Desktop Cowork support documentation and Cowork option in issue template #75)
• OS: Ubuntu 22.04 LTS, ARM64 (aarch64)
• Node.js: v22.22.0
• Plugin version: 2.8.10

Impact assessment:

• onnxruntime-node powers the embeddings system — without it, semantic search and similar memory lookup are completely unavailable
• sqlite-vec powers vector search — without it, vector-indexed queries fail
• Combined with better-sqlite3 ([Bug]: MCP Server fails to start in Claude Desktop Cowork environment (better-sqlite3 native compilation blocked) #73), this means all three native dependencies in the plugin are broken in Cowork

Proposed solution:
Apply the same prebuild strategy recommended in #73 to all three packages:

1. onnxruntime-node: Ship linux-arm64 NAPI binary via prebuildify or include the correct binary in the package
2. sqlite-vec: Ship linux-arm64 .so loadable extension via prebuildify
3. As a fallback, consider pure-JS alternatives where possible (e.g., @xenova/transformers with WASM backend for embeddings)

Related issues: #73, #74

[kevintseng]

Status Update - Deferred to Long-Term

This issue is being deferred to the long-term roadmap along with broader Claude Desktop Cowork support (#73).

Current Status

Phase 1 & 2 (PRs #78, #79) have resolved the immediate crash issues for CLI environments by implementing:

• Lazy loading for better-sqlite3
• Cloud-only fallback mode when SQLite unavailable

Why Deferred

1. Feature Usage: Current analysis shows onnxruntime-node and sqlite-vec are installed but not yet fully integrated into the main codebase

   • VectorExtension code exists but isn't actively used in production features
   • Embeddings system not yet critical path

2. Architectural Dependency: Full support requires the same cloud-first architecture as [Bug]: MCP Server fails to start in Claude Desktop Cowork environment (better-sqlite3 native compilation blocked) #73

   • Need Cloud API layer for embeddings operations
   • Need vector search via cloud backend

Future Solution Path

When Claude Desktop support is prioritized, this will be resolved through:

1. Cloud Embeddings Service:

   • Use @xenova/transformers (WASM-based, no native deps) as pure-JS alternative
   • OR: Cloud API for embeddings generation

2. Cloud Vector Search:

   • Vector operations via MeMesh Cloud API
   • No need for local sqlite-vec extension

3. Graceful Degradation:

   • Embeddings features disabled in cloud-only mode
   • OR: Transparently proxy to cloud service

---

For now: CLI users with better-sqlite3 installed can use vector features. Claude Desktop users should wait for cloud-first memory architecture.

Related: #73 (better-sqlite3), #77 (persistent storage)