[bin][parameter] Implement new parameter extraction scripts

Closes #959

See merge request !2933

Yue Wang authored 3 years ago and Timo Koch committed 3 years ago

Manual inputs are provided via a human-readable json file which is
under version control. The parameters.txt file is now completely
auto-generated and shouldn't be manually edited. All edits
happen to the json file. This makes sure formatting and data
are separated properly and git changes are minimal.

[fcstaggered] Various fixes

See merge request !2932

* outsideVolVars already contain Dirichlet values

[pnm][transmissibilityPatzekSilin] Clean-up and add assert

See merge request !2931

Fix BoundaryFlux class in pore network

Closes #996

See merge request !2869

Feature/initialize

See merge request !2928

[installexternal.py] Use dune release 2.8 per default

See merge request !2927

Feature/improve staggered gridgeometry

See merge request !2901

* write scvfs directly into vector using global index and fixed local indices
* add flag in scvf for processor boundary