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main: Pivot `/{decl}/file` to `/files` in config files

Eric Cousineau requested to merge EricCousineau-TRI/autopybind11:issue-93-file-spec into master

Resolves #93 (closed) (I think)

Well, at least this is the first step towards it. I think the whole "Let's optimize module compilation" can be done with source information that'll be available from pygccxml?

The YAML files were reformatted using the following script (with ruamel), 'cause I'm that lazy:
https://gitlab.kitware.com/EricCousineau-TRI/autopybind11/-/blob/4e71bfd174737b10c521eff099ea0459aa010731/tmp/ruamel_update.py

Edited by Eric Cousineau

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