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Restructure repo #806

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@edmundmiller

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@edmundmiller

Might break some stuff.

@jfy133 anythoughts on moving to a structure similar to the modules repo?

$ tree conf/utd_ganymede/
conf/utd_ganymede/
├── utd_ganymede.config
└── utd_ganymede.md

Maybe a better example

$ tree conf/uppmax/
conf/uppmax/
├── README.md
├── pipeline
│   ├── ampliseq.config
│   └── ampliseq.md
└── uppmax.config

Could nest the ampliseq one more time too.

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