Npm.install reify drops user dependencies from .opencode/package.json on Desktop start

Description

On OpenCode Desktop 1.18.27 (Linux), starting the app can silently remove user dependencies from a project's .opencode/package.json, breaking plugins (e.g. opencode-rag-plugin — RAG tools stop being registered without any error).

Root cause

In packages/core/src/npm.ts, Npm.install calls reify({ add, dir }) when:

1. node_modules is missing, or
2. package-lock.json does not cover all deps declared in package.json (checkDirty).

reify() runs arborist.reify({ add, save: true, saveType: "prod" }) where add contains only @opencode-ai/plugin@<version>. Arborist rewrites package.json/node_modules from the add list — any user dependency not in add is dropped. Verified: after a Desktop start, .opencode/package.json was rewritten to contain only @opencode-ai/plugin, and opencode-rag-plugin disappeared from node_modules; RAG tools (search_semantic, find_usages, ...) silently vanished from sessions.

Repro

1. cd <project>/.opencode && npm i opencode-rag-plugin (creates package.json with both deps).
2. Start Desktop 1.18.27 (or any build calling Npm.install on the .opencode dir) with node_modules missing or stale lockfile.
3. Check .opencode/package.json — opencode-rag-plugin is gone.

Expected

reify must preserve existing dependencies from package.json (all four sections: dependencies, devDependencies, peerDependencies, optionalDependencies) when rebuilding the tree.

Fix

Prepared in PR #47130 (commit "fix(npm): preserve existing dependencies on reify") — merges existing deps into the add list before reify, deduped by package name.