Built-in package manager vs manual ~/.atom/packages clone for pinned commits

A reproducible Atom editor setup requires choosing between the built-in package manager and manual installation into ~/.atom/packages for dependency control under a sunset registry.

The built-in manager provides UI discovery via the Atom package registry, automatic updates, and dependency resolution handled by registry metadata. Manual git clone into ~/.atom/packages allows pinning to a specific commit hash or using a local development version, but requires manual synchronization with upstream and manual resolution of peer dependencies.

Atom is sunset and the official registry and update servers may be unavailable or unreliable. The documented boot process loads packages sequentially, and mixed installation methods may interact with activation order and startup behavior.

Which approach preserves dependency metadata when the registry is offline? Does Atom treat manually cloned packages differently from manager-installed packages for activation order during boot? How can pinning be verified without triggering automatic update prompts from the built-in manager?