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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.

fixed an error introduced in
e2f37a30

Fix namespace name crystallisation -> crystallization

Avoid using namespace std in header files.

The reason is that the cpp files including that .h file
will automatically use namespace std

Added missing namespaces

These are the files generated automatically with the cmd
dictionaries. I renamed them to inc which is a more standard
extension for include files.

Almost is not anymore supported in v2.3

made version in "plumed config" consistent with the change
done in 2e4cee92

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This fixed a bug I introduced in 35ed62dc

Namely, now all the directories containing regtests should be explicitly listed
in regtest/Makefile. The result of the bug was that not all regtests were run

In the first job on travis-ci I set PLUMED_ALL_TESTS=yes

With this setting, if some of the regtests is not run the whole
test suite fails. This actually checks that all the optional modules
have been enabled at least in the first job of travis-ci

A section was not properly shown

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lapack and blas README files were not shown.

I guess this happened with some doxygen update that ignores README files.
Solved renaming to README.md.

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This reverts commit 366e00d6, reversing
changes made to 1cd9c350.