Root project indexing incorrectly excludes monorepo packages/ by default

[isaac10334]

What happened?

AiDex appears to hardcode /packages/ in DEFAULT_EXCLUDE for both init and update. That breaks normal JS/TS monorepos where packages/ contains the primary source code. This is super common.

This makes AiDex fail on a very common monorepo layout and forces awkward workarounds like indexing packages/ as a separate project.

Relevant source:

• src/commands/init.ts
• src/commands/update.ts

What did you expect?

packages/** should not be excluded by default, or this should be configurable/project-aware

Steps to reproduce

• Create a repo with source under packages/*/src/**
• Run aidex_init at repo root
• Run aidex_query or aidex_files for symbols/files under packages/**

Environment

• AiDex Version: 10.9.2
• Node.js Version: 20.13.1
• OS: Windows 11
• MCP Client: Codex (manual install)
• Language: TypeScript (pnpm workspace)

Error output / logs

[CSCSoftware]

Thanks for reporting! You're right — **/packages/** doesn't belong in DEFAULT_EXCLUDE. It's a workspace root, not a dependency folder.

Fix: Removed '**/packages/**' from DEFAULT_EXCLUDE in src/commands/init.ts. All other files (update.ts, session.ts) import from there, so the single-line removal fixes it everywhere.

Shipped in commit 1e17a0a — will be included in the next npm release.