Instead of using the `Assemblers` class to represent assemblers,
use the `Stage` class: The `Pipeline.add_assembler` method will
now instantiate and `Stage` instead of an `Assembler`. The tree
that the pipeline built is converted to an Input (while loading
the manifest description in `format/v1.py`) and all existing
assemblers are converted to use that input as the tree input.
The assembler run test is removed as the Assembler class itself
is not used (i.e. run) anymore.
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