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

I merge the patch --save-originals stuff on v2.0.
I am using it a lot and I think it is stable enough to go to v2.0.
This will allow to modify gromacs patch also in that version.

Conflicts:
	patches/patch.sh

Mode is redundant since:
* read or write can be decided depending if file is IFile or OFile
* append/non-append is decided based on RESTART option

Includes restart with METAD, READ and PRINT, and --multi

Files with gz extension are transparently compressed and decompressed.

Closes #17

There is a new function that is called after every regtest, before
comparing with reference. Can be used if files produced by plumed
need further post-processing

Added diagnostic

Possibility to set hills height using TAU as in the original
well-tempered metadynamics paper.

Addresses #56

There is no reason to avoid these values.

Addresses #56

(this file was removed)

Conflicts:
	user-doc/extract

    A large portion of extract was rewritten on master,
    I just redid the change I did on fix-69

I updated doxyfile to latest doxygen version. I also
enables the search engine. This required a small fix on the
extract script so that "action" pages receive a proper name
for the index.

I removed many graphs that were probably not useful
and were cluttering the output. Moreover, I
enabled the search engine and added an alphabetic
list of classes (classes -> class index)

Needed to have proper regeneration of links when new .h files are added.
I also added several comments.

Instead of using links to other source directories
we now use explicit include files. The approach is more
robust.

Closes #69

Now __PLUMED_INTERNAL_LAPACK and __PLUMED_INTERNAL_BLAS are
used as synonimous macros, consistently with the fact that either
both lapack and blas are internal or external

Conflicts:
	user-doc/Installation.txt

All libraries can be switched off with
./configure --disable-name

This allows testing or removing libraries that are
known to be buggy or problematic.

Notice that when lapack/blas are off, internal versions
are used (plumed does not work without them).

Also notice that when mpi search is on standard mpi compilers
are searched for before non-mpi ones.
Thus, to configure with mpi just type:

./configure

To configure without mpi use:

./configure --disable-mpi

I made this change since mpi is commonly needed and there is no
expected drawback from using mpi.

mostly for testing