JujutsuPatcher.apply_patch_for_empty_files() was matching all files

with "new file mode" in the diff, not just truly empty ones. After the

patch command correctly created new files with content,

apply_patch_for_empty_files() would then overwrite them via

make_empty_files(), truncating them to zero bytes.
The fix skips files that already exist on disk (created by patch) so

that only genuinely empty files (which patch can't handle) get

created.

Applied a patch that added new (non empty) files.
Ran unit tests.