I successfully created a File Decorator with an onAfterWrite() function that works fine if files are uploaded through the cms, but doesn't work from /framework/cli-script.php dev/tasks/FilesystemSyncTask. Is there a way to get the Decorator to be accessible there as well?

I added it to the config through yml:
File:
extensions:
- FileDecorator

and the decorator is:
class FileDecorator extends DataExtension {
...
}

does that FilesystemSyncTask work if you do it via the browser? http://localhost/dev/tasks/FilesystemSyncTask

Does running it in the CLI return any error messages?

Well, after reviewing the code in FileSystem::Sync() and Folder::syncChildren() it seems that the sync is done using raw queries which would explain why my onAfterWrite() extension isn't getting called from the sync. The onAfterWrite() did however work perfectly if the file was uploaded through the Assets Admin interface.

I worked around this by forking the FilesystemSyncTask and creating a custom task so I can do what I need once the sync is complete. Not as elegant as an onAfterWrite() but not much I can do since the sync functionality doesn't appear to be extensible.

I can probably understand the rationale behind using raw sql as it is probably faster than invoking the whole ORM part of the Framework (just less easy to write). If it's syncing a tonne of files and images from the file system this we be of benefit.