Fixes the diffs.

Updated the tutorial and its description in the handbook to use implicit instead of coupled and sequential instead of decoupled.

The general setDirichlet function takes two parameters (pvIdx, eqIdx)
corresponding to the index of the primary variable and the index of the
balance equation. A convenience function that only takes one parameter
exists which calls the general version with two equal parameters. So
far, this one parameter has been documented as equation index. However,
it is better to refer to the parameter as a primary variable index.

This commit changes the parameter name and improves the documentation.
Furthermore, it replaces calls in the tests, whenever the general
version was called with two parameters of different name but equal value
or whenever the simplified version was called with an equation index
instead of a primary variable index.

See FS#270 for details.

Reviewed by Timo.



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length = 150, thanks to kristopherg

reviewed by fetzer


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Fix a bunch of deprecation warnings.
Make plotoverline2d.hh more conforming to our style.
(reviewed by bernd)


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local variables.
Reviewed by Benjamin.


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Only public member names have been treated so far. Local variables
will be done shortly, classes maybe not before the next release cycle.
Everything old could be marked deprecated.

Reviewed by Benjamin and Christoph. 


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saturation. In particular, it deals with the capitalized "S"-indices: 
S0Idx -> s0Idx
SnIdx -> snIdx
SwIdx -> swIdx
SOrX1Idx -> sOrX1Idx
SOrX2Idx -> sOrX2Idx
SnOrXidx -> snOrXIdx
SwOrXIdx -> swOrXIdx 

Reviewed by Christoph. 



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in the old location by deprecated forwards to the new one. Adapt
includes. 
This implements FS #171. Reviewed by Markus.


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corrected minor inconsistency of decoupled tutorial with its docu (output interval too small). reviewed by Philipp

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introduces breaks to get all documentation in the code on a page in the handbook.

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   - we decided to keep the tutorials similar and to change them to
     start from a parameter file



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- new institute name
- add missing modelines
- reformat the entry for leopold stadler in air.hh

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decoupled 2p: fix compilation of tutorial and generalproblem, keep the property TwoPIndices for compatibility with box models, comment declaration of some unused variables

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There is no need to rush things. We agreed on first having the meeting
and then porting the change to the non-MpNc-models. Moreover, the change
has not been carried out according to what has been discussed at the
meeting. 
E.g. there was no completeState functionality of the models, and the simple
models also introduced parameter caches, although it was thought to not
necessarily having to do so.


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also call fluidState_.pressure() instead of
fluidState_.phasePressure() in the TwoPVolumeVariables.

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and the classes seem to be associated with the correct groups. 

Also improved documentation by getting rid of more than 250 Doxygen
warnings.


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Problems instantiated with Timemanager
TimeManager now runs the problem

update of handbook according to that.

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fix the GCC 4.6 stuff in a more backward compatible way and fix a lot of "variable set but not used" warnings on GCC 4.6

if the compiler doesn't know about constexpr

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