fix(manifest): flag backup files listed in the manifest but not stored

An incomplete iTunes backup still lists in its Manifest.db the files it
failed to acquire, so a module which found nothing for one of them looks
exactly like a module which found nothing on a device that never had the
artifact. The Manifest module now records a "missing" flag on those
records and reports the total, so a gap in the acquisition is visible in
manifest.json and in the command output.

The stored file IDs are collected by walking the backup folder once, which
keeps the check off the per-entry filesystem lookup path: on a 20k entry
manifest the module runs in the same time as before the change.

docs/ios/records.md

@@ -204,6 +204,8 @@ This JSON file is created by mvt-ios' `Manifest` module. The module extracts rec
 
 If indicators are provided through the command-line, they are checked against the original relative path in case. In some cases, there might be records of files created containing a domain name in their name, for example in the case of browser cache folders. Any matches are stored in *manifest_detected.json*.
 
+An incomplete backup still lists in its manifest the files it failed to acquire. Those records carry a `"missing": true` field, and the module reports how many of them it found. Use it to tell a module which returned nothing because the artifact was not acquired apart from one which found nothing on a device that never had it.
+
 ---
 
 ### `os_analytics_ad_daily.json`