Merge branch 'cmakeified' into msvtk

# By Ricardo Ortiz (27) and ricardo.ortiz@kitware.com (4)
# Via Ricardo Ortiz
* cmakeified: (31 commits)
  Change third party libs URLs to remotes.
  Fix bug in ibamr cmake file and linker flags.
  Fix small bug in samrai cmake file.
  Fix bug in samrai instalation instructions.
  Fix fortran file compilation macro.
  Tidy.  Add new instalation prefix to SAMRAI. "
  branch ibamr-cmake: Bypass SAMRAI configure script.
  Fix taget file placement.
  branch ibamr-cmake: Tidy.
  Tidy.
  branch ibamr-cmake: Fix bugs in CMake build system.
  branch ibamr-cmake: Minor changes.
  Fix minor bugs. Add configuration and use files. Also, added a gitignore file.
  Minor changes...
  Fix bugs in the cmake build system.CMake 2.8.8 should be used from now on since we depend on some of it features to build the single library. The External_QD tar.gz contain a mac file at the root that wont allow the external project to unzip properly.
  Tidy.  The build system is almost complete,  added qd and muparser as external projects.  IBTK builds and examples run succesfuly.  I need to clean the code so it is more compatible to the auto make build system(add a way to create IBTK_Config.h file in cmake).  Other small details need to be addresed but so far I can build IBAMR with cmake.
  Tidy
  Add fortran generation macro to IBTK. Tidy.
  Add CMake build system to IBAMR, calling the SuperBuild in IBTK.
  Tidy.  Added makefiles to build IBAMR lib.
  ...
Fix HDF5 url to point to version 1.8.9; bump up cmake version.

Fixes #1
The library needs cmake > 2.8.10 since it uses https for downloading
external libraries urls.
Fix compilation warning.  Add SAMRAI note at configure time.

Fixes #2
Tidy.
Add SetupForDevelopment.sh script to enforce some commit rules.

Closes #3
Add library dependency to superbuild