A working-tree scan (`status --scan` / `stage --scan`) already discards a
reverted uncommitted *file* add so `state_staged` matches the filesystem: a
file that was staged and then removed before any commit has no committed base
to delete from, so reporting a `Delete` would leave an unremovable "zombie"
entry. A reverted uncommitted *directory* add was not handled the same way.

Extend the same treatment to directories. When a directory node exists in
`state_from` but neither in `state_current` (never committed) nor on disk,
queue it for discard instead of emitting a meaningless `Delete`.

Discarding a directory node must also reclaim its subtree: `apply_pending_discards`
now recursively discards every child below a directory node before unlinking
the node itself, so no stale descendant slots are left behind.

Includes a Rust test covering the index-then-remove cycle for a directory add,
asserting the node is discarded (and does not resurface on a later scan) rather
than reported as a delete.

Signed-off-by: Huân Lê-Vương <[email protected]>

Move the is_nested_repository_root() check from the directory-walk loop
(where it runs for every item) into the unmatched-child arm of
binary_search_by, since a nested repository will never be tracked in the
current repository's merkle tree and therefore always falls there.

Normal directory descent (matched tracked nodes) now pays zero extra
filesystem metadata queries (no is_dir probes for .lore or .urc).

Preserve zombie-entry cleanup by restricting the check in the
matched `was_directory && is_directory` branch to the staged-only case
(scan_dirty && !current_node_id.is_valid_node_id()), where the cost is
already paid by other mutations. This prevents re-indexing of nested
repositories that were indexed before this boundary feature existed.

BEHAVIOR CHANGE: A nested repository directory that was *committed* into
the parent before this boundary check existed is no longer
auto-unmatched and will stay tracked until explicitly removed, matching
git's behavior with nested .git directories. Only staged (never-committed)
nested roots are auto-discarded on the next scan.

Add test case for the zombie-migration path: a staged directory that
becomes a nested repository root must be discarded and its contents not
re-indexed.

Signed-off-by: Huân Lê-Vương <[email protected]>