Fix Cloud uploads, sign-in persistence, and sync refresh

[adibhanna]

Cloud uploads could send empty bodies on iOS, long publications could time out after 30 seconds, and restarting the app could lose a saved Cloud sign-in. This fixes the native adapters, recovers credentials stored under the old Secure Storage prefix, and adopts the shared 2.50.0 publishing, conflict, and restore fixes from ZenNotes/zennotes#774.

• Preserve signed upload headers and supply Content-Type when absent so Capacitor sends the binary body; forward the intended timeout through both native timeout fields.
• Serialize Secure Storage initialization and migrate legacy credential/pending-sign-in records before use. Canonical credentials win, shared validation still applies, and logout cannot resurrect a legacy credential.
• Expose the metadata-only remote change probe so incoming changes refresh automatically without scanning local files or fetching attachments during the probe.

Validation: 93 tests pass; TypeScript, production web build, Capacitor sync, and signed iOS simulator build pass. Live native testing against zennotes.org covered sign-in/restart, automatic bidirectional sync, exact-hash 8.1 MB and 10,000,000-byte uploads, oversized-file recovery, publishing and updating the same URL (including Cloud Settings), offline conflict resolution, backup, restore, and unpublish. The final rebuild retained sign-in and received an Android-initiated restore: all eight files matched the checkpoint across iPhone, Android, and desktop, and a newer file disappeared on all three. Disposable Cloud resources were removed afterward.

Targets the existing release/1.9.9 baseline so this PR contains only the three Cloud fix commits. Shared source is pinned to 104416f560bb9e709620cabe9e1f225306f7a4ea. Native validation used a simulator; five-minute timeout forwarding is tested without deliberately slowing the live service for five minutes.