Index vectors were passed by value into the method and, additionally, copied element by element into new vectors, to remove the const attribute (which is no longer necessary), before calling the Epetra method. This resulted in two additional copy operations for each vector.

Disable compilation of  unmaintained_masstransport
Enable compilation of example_cavity and example_ML

Fixed compilation of example_ML, brought up-to-date with the changes from the Cleaning Week

void transformMesh( const function& meshMapping);
which move mesh points according to the mapping (function) meshMapping( Real& x, Real& y, Real& z).

comply with the new 0-based numeration for user defined functions

comply with the new 0-based numeration for user defined functions

fix the strongerFlag method to correctly
manage the NULL flag

add a parameter in the list from outside in SolverAmesos. In
particular, it will be possible to disable the verbosity of the
solver. 

2) Adding a new interface to access to the preconditioner

Force the code to recompute the variable-timestep BDF discretization
coefficient after initialization is done.

This bug was already present (but only latent) before the Cleaning Week.
The removal of the non-empty constructor made this bug to show up.

levelOfFill is used only by the IFPACK::ILU or IFPACK::IC, and it should be
a Integer value and not a double or Teuchos will raise an exeception.