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Yes, you can assign a project into a nested folder hierarchy. This feature is impressive but subtle.

Example:

Folder structure:
Home
-folder A
--folder b
---project A

to assign a task to project A from the inbox, tab over to the project field in the task, then start typing.

h:fa:fb:prA

then hit enter.

Depending on what your search results are as you type, you may have to change the letters that you type. However, you typically will not have to type out the entire folder/project.

You can also create a new project doing the same thing.
h:fa:fb:my new project
then command + enter

The only thing you can't do is assign an action into a projects hierarchy. I have a perspective that filters based on projects changed. I'll look at this perspective and move actions around in projects where I have a hierarchy and need to organize the actions.