Fix memory leak in LinSys_PETSC::gatherSolution

- need not to call VecCreateSequential, vector created by VecScatterToAll
- improve bin/valgrind.sh, allows passing additional parameters to valgrind

close #112
Merge branch 'JSI_bddc' into 1.8.1_patch
Substance ids renamed and moved as vector into SorptionBase.
Fix bug - wrong behaviour when unknown region is in input.
Copy DLL libraries into Cygwin install package.
Dual porosity test update.

- create new mesh - coarse square
- replace reference data
- compare with analytical solution (dual porosity only - dual_por.con)
Merge branch '1.8.0_master' of https://github.com/flow123d/flow123d into 1.8.0_master

Conflicts:
	bin/valgrind.sh
Time dependent parameter test (in 23) added for DualPorosity.
Cleanup in filed_intersection

- remove dead code
- move ngh interface to separate header file
Merge branch '1.8.0_master' of github.com:flow123d/flow123d into 1.8.0_master
Cleanup in global_defs

- remove obsolete macros, leavin just ASSERT and DGB* macros
Fixed internal links in reference manual.
Fixes #159.
Fix detection of fetch URL.

Close #155.
Remove get_solution_vector and get_parallel_solution_vector.

- empty implementation of these in EquationBase
- removed from descendants (transport, reactions)
- clean ReactionTerm class
Avoid misleading message from "ulimit" command.
Remove debug messages.
Creating help for PETSc parameters.

- add support for redirecting whole PETSc output
- add make rule to run flow123d and extract PETSc help
Merge branch 'master' into 1.8.0_master

Conflicts:
	src/flow/darcy_flow_mh.cc
	src/la/linsys_BDDC.cc
	src/la/linsys_BDDC.hh
EquationBase methods empty implementation.

- virtual methods are empty and gives debug message if called unimplemented
- add method initialize()
- remove EquationNothing
- set flag equation_empty_ if default constructor is called
correct name of the member function