feat: add configurable dependency trace root

[yimingjfe]

Summary

• add a first-class traceRoot option to nodeDepEmit
• resolve relative roots from appDir while preserving the existing / default
• use the same canonical root for nft tracing, traced-path restoration, and dependency classification
• keep base owned by nde while forwarding other nft options and filesystem hooks
• document the new option and add a patch changeset

Motivation

A configurable trace boundary lets callers narrow nft dependency analysis instead of always tracing from the filesystem root. Keeping tracing and path restoration on the same base prevents nft's relative results from being resolved against a different root.

Scope

This change configures nft's base and keeps nde path restoration and dependency classification aligned with it. Entry discovery, package lookup, output paths, and existing hook semantics remain unchanged.

Validation

• pnpm test
• pnpm build
• Vitest: 11 tests passed
• Node release tests: 8 tests passed
• Biome commit hook
• git diff --check