tests: add kw only_failed to `runtests` command (!205)

Unify interface for LGL and GLGL rules and update `SpectralElement` accordingly:
- most routine should just work with one argument `Npts`
- add more doc strings
- remove unused methods `linear_dependency_matrix` and `expansion_matrix`
- remove unused fields of `SpectralElement`

GRHD: fix another edge case where c2p_set_atmosphere_on_failure should overrule (!203)

dg1d: substep callbacks have to be evolved after updating the solution (!202)

dg1d: update `lgl` and `glgl` integration methods (!201)

- put the integrand as the first argument
- add integration methods that can work with a function argument
- add doc strings
- update usage of `integrate` functions in rest of code

GRHD: fix atmosphere freezing and evolution logic (!199)

Fixes the following issues with the current implementation:
- `update_atm_domain_of_dependence!` did not distinguish between points
  1. whose neighbors are also in the bulk,
  2. where one neighbor is on an interface,
  3. where the point itself is on an interface.

  These cases are already properly handled in 2d.
- `stop_atmosphere_evolution_*` methods did not account for the `c2p_freeze_atm` flag, which essentially prevented the atmosphere to ever evolve.
- `update_atm_domain_of_dependence!` was activated by setting `c2p_dynamical_atm`, but it should be controlled by `c2p_enforce_causal_atm`



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Additional fixes with less impact:
- remove unused parameter `id_atmosphere_density` from `GRHD` section
- `c2p_set_atmosphere_on_failure` should really suppress any errors appearing in the cons2prim

I am surprised that I did not need this before.

This is intentionally a hacky implementation as I just need that for the thesis right now.

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This also implements
- the total rest-mass computation for the GRHD project as a first application,
- adds helper functions for the `Output` struct to read all data at once.

Fixup to !193

GRHD: add tov symmetrization for all DG rhs' that use the spherical1d (!195)

dg1d: make `main` accept paths to output directories (!196)

dg1d: do not strip trailing newline chars as this might corrupt git patches (!194)

dg1d:  allow parameter overriding on cmd line (!193)

Allows to use `main(parfile, "Mesh.n" => "1")` to override the value given in the parfile.

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To do this we
- parse the TOML file
- flatten the dict-of-dicts to a single dict with the keys joined by a `.`
- insert the parameters
- unflatten the dict to a dict-of-dicts
- write this to the output directory

Unfortunately, `TOML.jl` does not allow to parse into `OrderedDict`.
This causes the newly written parfiles to be messed up.
Furthermore, by manually re-writing the parfiles we also do not preserve any comments or formatting.

dg1d: Avoid generating nested output folders in case parameter file comes from inside an output folder (!192)

GRHD: add toggle to allow AV to sense based on the log10 of the variable (!190)

Adds a new parameter to the `GRHD` section:
- `av_sensor_logabs_D`: If `true` apply the AV sensor to `log(|D|)`, otherwise use `D`, where `D` is the state variable for the rest-mass density (including the volume factor).