Two code paths were appending silo/manifest.json to the ZIP without
removing the previous entry, causing Python's zipfile module to warn
about duplicate names:
1. slotFinishSaveDocument() re-injected the cached manifest from
entries, then the modified_at update branch wrote a second copy.
2. update_manifest_fields() opened the ZIP in append mode and wrote
an updated manifest without removing the old one.
Fix slotFinishSaveDocument() by preparing the final manifest (with
updated modified_at) in the entries dict before writing, so only one
copy is written to the ZIP.
Fix update_manifest_fields() by rewriting the ZIP atomically via a
temp file, deduplicating any pre-existing duplicate entries in the
process.
