This is a huge commit, applying indentation to the whole
code.

See #215

Given header file.h, it is good practice to have a file file.cpp
that includes it as first header.

I just fix the order of includes here. There are still several
headers which do not have a corresponding cpp file, and also
a few that are not included anywhere (which is obviosuly an error).

I will fix them in a later commit.

This barrier is apparently useless since it comes
just before a Bcast.

Anyway, it looks like it is solving an issue that appeared on
TRAVIS (at least on my laptop) so I add it here.

Related to #183

It is now possible to enforce the suffix of a file.
Additionally, there is a check so that files named "/dev/null"
are not added any suffix nor backed up.

These changes are useful to implement single-file multiple walkers

Allow individual action to set restart, using RESTART=YES or
RESTART=NO. By default, RESTART=AUTO, that means that global
restart settings are used.

Notice that this required to change the way OFile knows about
restart. Indeed, if the file is linked to an action,
it should use Action::getRestart instead of PlumedMain::getRestart.

Can be useful if one wants to open externally a file
but generate the name with PLUMED rules
and properly use backups/append.

Now upon rewind file is moved on a backup name (bck.last.xxx).
This is to have a recover file in case of crashing while checkpointing

Files with gz extension are transparently compressed and decompressed.

Closes #17

(thanks to Toni Giorgino)

I fixed a missing include.

Original comment:
Fixes in backup output files - cant rename open file under windows - print reason for failure - remove leak of FILE*s

(cherry picked from commit 448e84fc)

(thanks to Toni Giorgino)

I fixed a missing include.

Original comment:
Fixes in backup output files - cant rename open file under windows - print reason for failure - remove leak of FILE*s

I set it to 2 instead of 2.0, so that it will not be necessary
to update it

Removed many scans of the output buffer by keeping trace of buffer length.
Time needed to write a long line with a sequence of file.printf() is
now linear with line length. Before it was quatradic, causing problems
especially when logging huge atom lists at startup.

I replaced everywhere it made sense the new Communicator class
syntax. This commit is not strictly necessary, but provides
examples of the simpler syntax so I think should be merged

In analysis runs results from previous analysis are saved as
analysis.0.<filename>, analysis.1.<filename> etc.  If the calculation
is NOT restarted and there are files with these names hanging about they are
renamed bck.0.analysis.0.<filename> bck.0.analysis.1.<filename> etc.

Having the backup string specified in OFile::open leads to clashes
with the routine that sets open using w+, w, rw etc.  It is thus changed
so that you can set the backup string to use with a separate method in the class

Made it so that virtual routine is not called from constructor.  If the calculation
is terminated during the analysis phase then the analysis is now restarted when
the calculation reaches update on the first loop.  I also removed the duplicated
backup code that was in analysis.  Backup is now done by the routines in OFile.
This routine is now a little more flexible in that you can specify the string
in the backup name.

Allows to switch off auto backup or to change the maximum number of 
backups