Fixed geometry.jou to be consistent with mesh.
Reduced mesh size for quicker runtimes.
Cleanup APREPRO lines in journal files.
Cleanup of journal files.

Move common settings to pylithapp.cfg. Reduce total time to 100*yr.
Changed comments to provide relaxation time.
Refine tolerances and scales.
Small tweaks to tolerances.
Added spatial database to Makefile.am so it will be included in
distributions.
Cleaned up gravity example, and hopefully have stable solution for
finite strain problem. New version uses symmetry and small time step
to stabilize finite strain example.
Modified the README to reflect the new layout of the examples.
Removed old mesh file from Makefile.
Finished putting together gravity example.
Added new pvsm files for scaled and unscaled velocity vectors, and
added cases for no initial stresses.
Made changes to makefiles for new files.
Merge branch 'williams/add-examples-grav2d' of github.com:geodynamics/pylith into williams/add-examples-grav2d
Merge branch 'baagaard/feature-progress-monitor'

* baagaard/feature-progress-monitor:
  Fix update conditions.
Merge branch 'baagaard/feature-output-station-names'

* baagaard/feature-output-station-names:
  Added station names to documentation.
  Add station names to examples with OutputSolnPoints.
  Added testing of OutputSolnPoints to 3-D full-scale test.
  Add testing of OutputSolnPoints to full-scale test.
  Use list for station names.
  Added output of station name at Python level.
  Added unit tests for writing point data with DataWriterHDF5Ext.
  Finished C++ implementation of writing station names.
  Switch to fixed length string dataset in HDF5 to allow parallel I/O.
  Add station name to list of points for output.
  Small improvement to unit test.
  Add writePointNames() to DataWriter.
Merge branch 'willic3/fix-plasticity'

* willic3/fix-plasticity:
  Fixed makefiles for 3-D plasticity test.
  Cleanup of 3-D plasticity test.
  Cleanup of Makefiles for creating source distribution.
  Cleaned up cfg files and dir structure for 2-D plasticity test.
  Updated userguide to describe feasible stress state.
  Added 2D version of plasticity test and moved existing plasticity tests down a level. They probably need updating.
  Added missing makefiles.
  Modified Drucker-Prager for the case where there is no plastic yield and tensile yield is not allowed.
  Added test for plasticity + initial stress (3d).
  Some changes to plasticity section plus changed version of LyX to older version.
Merge branch 'williams/add-examples-grav2d'

* williams/add-examples-grav2d:
  Made changes to makefiles for new files.
  Finished putting together gravity example. Added new pvsm files for scaled and unscaled velocity vectors, and added cases for no initial stresses.
  Removed old mesh file from Makefile.
  Modified the README to reflect the new layout of the examples.
  Cleaned up gravity example, and hopefully have stable solution for finite strain problem. New version uses symmetry and small time step to stabilize finite strain example.
  Added spatial database to Makefile.am so it will be included in distributions.
  Small tweaks to tolerances.
  Refine tolerances and scales.
  Changed comments to provide relaxation time.
  Cleanup of journal files.
  Cleanup APREPRO lines in journal files.
  Reduced mesh size for quicker runtimes.
  Fixed geometry.jou to be consistent with mesh.
Merge branch 'master' of github.com:geodynamics/pylith

* 'master' of github.com:geodynamics/pylith: (43 commits)
  Fixed makefiles for 3-D plasticity test.
  Cleanup of 3-D plasticity test.
  Cleanup of Makefiles for creating source distribution.
  Cleaned up cfg files and dir structure for 2-D plasticity test.
  Updated userguide to describe feasible stress state.
  Added 2D version of plasticity test and moved existing plasticity tests down a level. They probably need updating.
  Added missing makefiles.
  Modified Drucker-Prager for the case where there is no plastic yield and tensile yield is not allowed.
  Added test for plasticity + initial stress (3d).
  Some changes to plasticity section plus changed version of LyX to older version.
  Added station names to documentation.
  Add station names to examples with OutputSolnPoints.
  Fix update conditions.
  Added testing of OutputSolnPoints to 3-D full-scale test.
  Add testing of OutputSolnPoints to full-scale test.
  Use list for station names.
  Added output of station name at Python level.
  Added unit tests for writing point data with DataWriterHDF5Ext.
  Finished C++ implementation of writing station names.
  Switch to fixed length string dataset in HDF5 to allow parallel I/O.
  ...

Conflicts:
	examples/2d/gravity/Makefile.am
	examples/2d/gravity/deform_view.pvsm
	tests/2d/plasticity/Makefile.am
Added tutorial for grav2d and put Makefile.am back in
gravity example output directory (there are two .pvsm files in there).