Added fixes to checkpoint writing in analysis

Checkpoint is appended in restart mode and overwritten when opened at
start of calculation with no restart or when analysis is completed.  Most
of this is looked after within OFile now
Fixed small things in analysis

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.
Removed clash in OFile in previous commit.

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
Changed optimization for one function

OptimalAlignment::weightedAlignment crashed with intel c++ -O3.
I was not able to find why (gdb and valgrind did not help).
With this workaround, that function only is optimized at -O2 anyway.
Better backup of old files in analysis routines

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.
Merge branch 'v2.0' of git.assembla.com:plumed2 into v2.0
Changed default install path to /usr/local

This is the standard path for linux distribution. Thus "make install"
will fail unless run with root permission or unless PLUMED_PREFIX is
explicitly set. I also fixed DYLIB path for mac (plumed path
should be prepended)
Changed reference to plumed 1 paper

I moved the reference together with the others (using cite()) so that
it is more visible. I also updated a bit the description
Better modulefile

* check that PLUMED_KERNEL is not redefined
* disable paths for libraries if plumed is statically compiled

Also fixed "make uninstall" so that it always clean up dynamic libraries
Merge branch 'v2.0'