refactor: improve code

[nainglinnkhant]

Note

Medium Risk
Touches core CLI execution paths (logging streams, option parsing, upload/sync concurrency), which could affect user-visible behavior and throughput; changes are localized and covered by updated tests but warrant manual smoke-testing of piping and large uploads.

Overview
The CLI now keeps stdout clean for piped output by routing @clack/prompts logging/spinners through a new utils/logger (stderr), and the update-checker is made non-blocking and prints its banner to stderr after command execution.

Command option handling is simplified by removing the custom mergeCommandOptions helper in favor of Commander’s optsWithGlobals(), and completion install/uninstall error paths now exit non-zero.

Upload/sync hot paths are modernized: file reads/stats are moved to async fs/promises, uploads switch from batch-by-batch to sliding-window concurrency via p-limit, manifest uploads can optionally show per-file strategy, and --unique dedup logic is extracted into shared checkExistingFiles. Output formatting is tweaked so formatBytes(undefined/NaN) returns "-", and saveConfig writes atomically; dotenv is removed from CLI dependencies.

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