docs(functions): merge manual-only examples and notes into headers

Folds the examples Section 5 carried but the headers did not into each
function's `# EXAMPLE`, and moves the three lines that only looked like
examples -- the two typo-abbreviation notes and rm's /usr/bin/rm fallback --
into `# NOTES`, the label already in use.

Also corrects gi's synopsis, which omitted -l, and documents yt-dlp's
--no-embed-thumbnail in `# ARGUMENTS`.

functions/ls.fish

@@ -16,6 +16,8 @@
 #
 # EXAMPLE
 #   ls ~/projects
+#   ls
+#   ls -a ~/projects
 function ls --description 'List all files'
     # Opinionated guard (C1): fall back to bare command ls when disabled.
     if not __fish_config_op_enabled __fish_config_op_aliases