using templates to avoid duplicate functions

[gridmanager] Add const overload for grid

See merge request !3635

[io][grid][sub] Binary mask reader

See merge request !3630

When setting the parameter Grid.KeepOnlyConnected to X, Y, or Z,
we only keep cells that are connected to __both__ boundaries in
that direction.

[multidomain] Fix updateAfterGridAdaption

Closes #1296

See merge request !3634

[io][grid] Geometry and reference element are returned by value

See merge request !3636

[io][grid] Add function for updating a subgrid.

See merge request !3633

[porenetwork][util] Fix trimming of porenetwork in extraction script

Closes #1295

See merge request !3632

[cleanup] Remove deprecated code related to solvers and brineCO2

See merge request !3622

Improve error message for untracked files in make_installscript.py

See merge request !3544

[bin][installexternal] use composition for TarSafe

See merge request !3628

[bin][installdumux] Use logger to print to file and stream simultaneouly and add progress symbol

See merge request !3625

Kudos to Christoph Grüninger for the suggestion
to improve the log file output an initial implementation!

[docs][doxygen] Add former handbook chapter directory structure to doxygen

See merge request !3567

Resolve "[PNM][util] Check for versions of porespy and openpnm in python scripts + updating scripts to new versions"

Closes #1243

See merge request !3565

Merge branch 'feature/ff-pm-coupling-allow-different-discretizations-easy-to-read-commit-history' into 'master'

[ff-pm-coupling] allow different discretization schemes

See merge request !3620