add .prm.out files to make eclipse happy

Even though the .out files get generated by the Makefile in doc/ when
you build manual.pdf, it turns out eclipse is complaining when the .out
files are not present.
Also remove the .out from .gitignore again and do not generate a .out
for doc/manual/empty.prm because it is not used.
Add remove 'all' as a possibility for model names and other plugins.
Merge pull request #102 from bangerth/fix-defaults

Add remove 'all' as a possibility for model names and other plugins.
multiplex output

All output is now also put into output/log.txt in addition to the
screen.

Some error messages are now only printed on processor 0 instead of on
every processor.

The header should be printed in case of early failure (for example no
prm given), but also piped into the output file. For that reason it now
lives in global.h. Update the version script to find the version info.
update changes.h
Merge pull request #103 from tjhei/multiplex_output

multiplex output
Do not create output from processes != 0 if there is an error in the input file.
Write a changelog entry.
Merge branch 'fix-massively-parallel-error-message' of https://github.com/bangerth/aspect

this closes pull request #104.
fix ambiguous if/else statement
Fix the issue reported by Ian where an MPI implementation does not offer MPI_C_BOOL.
fix some TODOs
fix pressure normalization
add test
Merge pull request #105 from tjhei/fix_a_couple_of_todos

Fix a couple of TODOs
Merge pull request #107 from bangerth/fix-MPI_C_BOOL-issue

Fix the issue reported by Ian where an MPI implementation does not offer...
fix tests broken in 46893f6

It turns out that the change to log stuff into output/log.txt changed
the order of the header and the message of loading shared libs, which
broke 40 tests. This fix restores the original order and only prints the
header into the logfile as soon as that one is set up.
tests: numdiff should treat comma as a separator

This fixes parsing number of the form
 "Errors u_L1, p_L1, u_L2, p_L2: 1.274730e-02, 3.576354e-01"
correctly.
fix test outputs

A couple of tests changed slightly due to a different quadrature order
used in the KellyEstimator.
rework linear solver tolerance

Change the Stokes linear solver tolerance to inlcude the current
pressure instead of only the rhs. In the past the formula for the Stokes
solver tolerance was:
   rhs.l2_norm() * parameters.linear_stokes_solver_tolerance

This causes problems if the magnitude of the rhs is large (for example
due to a large gravity vector) and if the current pressure solves the
problem fairly well (so the initial residual is much smaller than the
tolerance as defined above). This is basically caused by the static
pressure being a good solution. The new formula is:
  || B^T p_0 - G || * parameters.linear_stokes_solver_tolerance

This fixes the problem that one had to use a linear solver tolerance of
1e-15 to make convection_box.prm work.