Greptile Summary

This PR is a documentation-only change that clarifies the distinction between project-level cleanup (aube prune) and global store cleanup (aube store prune). All changes are limited to help text, doc comments, and generated documentation files — no runtime behavior is modified.

• aube prune now describes its lockfile-driven algorithm, lists what it removes (stale top-level links, virtual-store entries, dangling .bin links), and explicitly states it does not modify package.json or the lockfile, with a cross-reference to aube store prune.
• aube store prune gains a detailed description of its scope (the store from aube store path only), its reachability model, and the hardlink-vs-reflink (APFS/btrfs) caveat about link-count reliability.
• Changes are propagated consistently across aube.usage.kdl, Rust source doc comments, the generated commands.json, and the rendered Markdown docs.

Confidence Score: 5/5

Safe to merge — all changes are help text and documentation strings with no runtime logic touched.

Every change is limited to doc comments, string constants, KDL help blocks, generated JSON, and Markdown files. The wording is accurate and consistent across all eight changed files, and there are no modifications to executable code paths.

No files require special attention.

Important Files Changed

_{Reviews (2): Last reviewed commit: "docs: clarify prune commands" | Re-trigger Greptile}