apply equalize_atmosphere_spherical1d in correct branch of callback

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).

Evolve: align stepper logic between all ERK implementations (!189)

This assumes that the first row in the `a` matrix of the Butcher tableau for ERK methods has only zeros, which seems to be the case for the all the methods have atm.

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Problem explanation:

So far the LSERK4 and the remaining ERK steppers worked slightly different.
The former used for the first substep the initial data array `u0`, and `u!`  for the remaining steps. That shortcut avoids a copy and appears natural for the LSERK4 algorithm.
OTOH, in the ERK stepper we first copy `u0` into `u!`, then accumulate some substep `k`s into `u!`, and then call the RHS with `u!`. (the reason we always copied `u0` over was that we did not account for the above assumption on `a` before)

The problem was now that in the GRHD evolutions we sometimes alter the state vector in the RHS computation.
This influenced the results to the extent that we could not run the (newly added) reftest only with the LSERK4 method.
What was happening was that when using the ERK method we never altered `u0` directly, only `u!`, whereas `u0` was altered in case the GRHD RHS decided to do so on the first step.
Subsequent substeps of the ERK method depend upon `u0`, and so this broke things.

GRHD: ban `ParameterDB` usage from `rhs` due to type instabilities (!188)

GRHD: enable `bc = from_id` for dynamic Bondi accretion test (!187)

ScalarEq: adds the av_recompute_substeps option (!186)

In analogy to how its done for SRHD.

Adds the following parameter to the `ScalarEq` section:
- `av_recompute_substeps`: If `true` then all callbacks related to `HRSC` are ran in substeps of the time stepper.

ScalarEq: Fix time step computation for DG method (!185)

similar !183

ScalarEq: Implement general slope limiter methods (!184)

Reuses the implementation from `SRHD`.

The following parameters are added/updated to the `ScalarEq` section:
- `hrsc` (updated): added option `slope_limiter`
- `slope_limiter_method` (new): similar to `SRHD.slope_limiter_method`
- `slope_limiter_method_tvb_M` (new): similar to `SRHD.slope_limiter_method_tvb_M`

SRHD: Use correct timestep scaling for vanilla DG (!183)

Evolution: fix substep callbacks shall be called after rhs evaluation (!182)

I haven't used substep callbacks much, so this should not have an effect on current experiments.

GRHD: Make AV method work with sperical1d (!181)

Move some methods to were they belong.
And also enable AV method to work with the spherical1d formulation.

GRHD: Add option to disable the cartoon derivatives when running with the cartoon formulation (!180)

Adds the following option to the `GRHD` section:
- `doublecartoon_disable_derivatives`: If `true`, then the doublecartoon derivative terms are not added to the source terms.

It appears that this option is senseless, because why even use the doublecartoon formulation in the first place.
However, it turns out that these derivative terms severely degrade the quality of any TOV star tests I tried so far,
and removing those terms from the equation helps a ton. The reason is likely that these terms contain 1/r (or 1/x) factors
which will amplify any noise coming from the TOV star's surface and propagating inwards.

Note that removing those terms changes the PDEs we solve.
In fact, removing these terms was already considered in Bugner's paper Physical Review D, 2016.