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storage/_casbaseddirectory.py: Implement `_apply_changes`

Tristan Maat requested to merge tlater/CASdiff into master

Description

This is part of the work for #985 (closed); we introduce a _merge directory for CasBasedDirectorys, so that they can be merged into each other as part of our workspace algorithm.

This will be part of !1726 (closed) and depends on !1761 (merged).

Edited by Jürg Billeter

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