Yeah, the structure of a localization target is pretty much expected to be in this format (assuming an “en” and “fr” culture):
* {TargetName}/
* {TargetName}.manifest
* en/
* {TargetName}.archive
* {TargetName}.po
* {TargetName}.locres
* fr/
* {TargetName}.archive
* {TargetName}.po
* {TargetName}.locres
It used to be a little more flexible, but over time we’ve moved towards this consistent layout, and moving forwards this will be the required layout. I’d recommend adjusting your target to conform to this layout to avoid any future issues.
With regards to the config files generated via the Localization Dashboard, those are only used by the gather commandlets (not the dashboard itself). The commandlets and the dashboard currently have two completely separate configuration layouts for a target, although I plan to unify these at some point so that both work on the same set of data.
For this reason it’s recommended to use the localization dashboard to manage your localization targets, as I will make sure the data there upgrades automatically, however any manual commandlet INI files will need a manual port.