Fix source-linked upgrades and MCP array schema

[ArshyaAI]

Summary

• replace source-linked upgrade git pull --ff-only with explicit clean-worktree fetch/merge handling for tracked, no-tracking, fast-forward, and clean custom-branch merge cases
• keep git/bun subprocess calls on execFileSync array args and surface the actual auto-upgrade error before manual recovery guidance
• add the missing items: { type: 'string' } schema for extract_facts.entity_hints so OpenAI-compatible function schema validation accepts the MCP tool definition

Tests

• bun install --frozen-lockfile
• bun run typecheck
• bun test test/mcp-tool-defs.test.ts test/upgrade.test.ts
• HOME=/private/tmp/gbrain-test-home bun run test (repo tests write to ~/.gbrain, so HOME is redirected to writable temp space)

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