fix(cli): support flat standalone dependencies

[Aymericr]

Summary

• allow runtime staging when a clean standalone build already has flat dependencies and no Bun linkage directory
• preserve real filesystem errors instead of silently treating them as optional directories

Verification

• bunx biome check packages/cli/scripts/stage-runtime.ts
• bun run --cwd packages/cli check-types
• bun test packages/cli/src (20 passed)
• bun run --cwd packages/cli prepublishOnly
• packed-tarball smoke from a synthetic flat standalone runtime with no .bun/node_modules

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Note

Low Risk
Small change to optional-directory handling in the CLI packaging script; no auth, data, or runtime behavior changes beyond avoiding false failures on flat layouts.

Overview
Runtime staging now tolerates standalone builds that already ship flat node_modules and lack Bun’s .bun / .bun/node_modules layout.

removeUnusedSharp and flattenBunNodeModules no longer treat every readdir failure as “optional”: only ENOENT is ignored; other filesystem errors propagate so real staging problems aren’t swallowed.

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