fix(memory): SQLiteBackend schema migration + memory_store metadata support

[dskarasev]

Summary

Two related bugs that together make AutoMemoryBridge.syncToAutoMemory() always return 0 entries when the database was created by MCP tools.

Bug 1 — SQLiteBackend crashes on DB created by the MCP sql.js backend

createSchema() uses CREATE TABLE IF NOT EXISTS but never migrates existing tables. When .swarm/memory.db is first created by MCP tools (sql.js backend — memory-initializer.ts), the table is created with a different DDL that lacks columns access_level, version, and "references". Subsequent calls to rowToEntry() crash with:

SyntaxError: "undefined" is not valid JSON
  at SQLiteBackend.rowToEntry (sqlite-backend.js:537)

Fix: after CREATE TABLE IF NOT EXISTS, run PRAGMA table_info and ALTER TABLE ADD COLUMN for each missing column (safe no-op if column already exists).

Bug 2 — memory_store MCP tool discards metadata, breaking AutoMemoryBridge sync

storeEntry() hardcodes '{}' as metadata regardless of caller input. The memory_store MCP tool has no metadata parameter in its input schema. Because AutoMemoryBridge.queryRecentInsights() filters on metadata.confidence >= 0.7 (default minConfidence), every entry stored via MCP is permanently excluded from sync — syncToAutoMemory returns 0 even when the DB contains many entries.

Fix:

• Add optional metadata parameter to memory_store input schema (documented as needed for AutoMemoryBridge)
• Add metadata to storeEntry() options interface
• Pass metadata through to the INSERT instead of hardcoded '{}'

Reproducer

# Store something via MCP
mcp__claude-flow__memory_store key="test" namespace="learnings" tags=["insight"] value="..."

# Run sync — observe "Synced 0 entries" despite DB having entries
node .claude/helpers/auto-memory-hook.mjs sync

Files changed

• v3/@claude-flow/memory/src/sqlite-backend.ts — schema migration in createSchema()
• v3/@claude-flow/cli/src/memory/memory-initializer.ts — metadata option in storeEntry()
• v3/@claude-flow/cli/src/mcp-tools/memory-tools.ts — metadata param in memory_store schema

Test plan

• Create a fresh DB via MCP memory_store → verify SQLiteBackend.initialize() no longer throws
• Store entry with metadata: { confidence: 0.9 } via MCP → verify syncToAutoMemory() returns it
• Store entry without metadata via MCP → verify existing behaviour unchanged (empty metadata {})
• Run on existing DB with all columns present → verify ALTER TABLE no-ops silently

🤖 Generated with claude-flow