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plumed info --user-doc and --developer-doc now fall back
to online doc if local doc is not installed

Fixes #240

It should make linux, brew, and port builds faster.

Generates partial tgz files and checksums for macports

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Apparently required for install_name_tools to work on 32 bit systems.
Notice that this is redundant when installing with MacPorts.

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This fixes the hardcoded path on dylibs

This flag disables the autoconf tests related to static patching.
The rationale is to be 100% sure that a wrong c++ library could not
be accidentally linked.

Notice however that this does not disable the "plumed patch --static"
flag. I think this should be fixed for the procedure to be more robust.

In the future, we could make this flag disabled by
default (to discourage static patching). Meanwhile, this is an option.

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Using INTEL compiler with optimization leads to problems in
LatticeReduction class when using large simulation boxes. I now
changed the thresholds from absolute to relative, and this seems to
solve the problem

Fixed a longstanding bug affecting EXTENDED_LAGRANGIAN and
METAD with ADAPT=DIFF when having arguments with periodicity
such as (min,max) with min+max!=0

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This fixes a problem in the way atoms are setup for calculations where you take an input
from a multicolvar filter as input to a new multicolvar if SPECIESA and SPECIESB are used.
For instance you might be calculating Q6 for those atoms that have a coordination number
greater than 4

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Notice that almost all files were updated with the astyle commit
2813d759

Year in header is here updated to 2017