Upgrade: Fix updating plugins which include a numeric file/folder names.

The fix in [41821] caused numeric folder names to be reindexed to 0..n when in the root directory (for example, `my-plugin/24/`).

Props edo888.
See #41524.
Fixes #42628 for trunk.

Built from https://develop.svn.wordpress.org/trunk@42214


git-svn-id: https://core.svn.wordpress.org/trunk@42043 1a063a9b-81f0-0310-95a4-ce76da25c4cd