Document REST DELETE limitation: files only, empty folders orphan on disk

Learned removing the retired archive/ and _agent/outputs/ trees: DELETE
cannot remove directories; the last-file deletion leaves empty folders
that the REST listing 404s (falsely reading as gone) while Obsidian
still shows them — manual cleanup required. Noted in api-reference.md
(Deleting Files) and linked to the TODO-1.6 retired-tree lint item.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

echo-memory.plugin.src/skills/echo-memory/references/api-reference.md

@@ -197,6 +197,13 @@ curl -s -X DELETE \
 
 Only on explicit operator request. Deletion is destructive.
 
+> **DELETE removes files only — never directories.** Deleting the last file in a folder
+> leaves the empty folder orphaned on disk; the REST listing then 404s (nothing left to
+> list), which falsely reads as "the tree is gone", but Obsidian's file explorer still
+> shows it. After removing a folder's last file, tell the operator the empty folder
+> needs manual deletion in Obsidian — do not claim the tree is gone from a 404 listing.
+> (Learned 2026-07-03 removing the retired `archive/` and `_agent/outputs/` trees.)
+
 ---
 
 ## URL-Encoding Notes