fix(pipeline): a file named nul no longer aborts every index run on Windows

On Win32 `<dir>\nul` opens the NUL device, so the control-file scan of the
semantic manifest could not inspect a file Git Bash creates from `cmd > nul`,
failed the whole manifest, and every index_repository returned
aborted_previous_preserved (upstream issue DeusData#2646, reproduced locally with the
CLI). The scan now inspects only directories and control-file names and skips
the rest by the listing's own type; on POSIX an entry of unknown type is still
inspected, keeping the manifest fail-closed.

Regression test fails before the fix (rc -1) and passes after; the CLI indexes
the reproduction repository.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Signed-off-by: SanHsien <34234698+SanHsien@users.noreply.github.com>

Author: SanHsien