Remove libsodium and lowdown submodules to fix recursive clone

These submodules were causing failures during recursive git clone
operations. The submodule entries were still registered in the git
tree even though they were removed from .gitmodules, causing:
"fatal: No url found for submodule path 'external/lightning/external/libsodium'"
and similar errors for lowdown.

This removes both submodule references from the git index to resolve
recursive submodule initialization failures (exit code 128).

Changelog-None

Author: erickcestari