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In 84ad8d2a a bug was introduced and
manual was not correctly pushed from travis-ci

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(cherry picked from commit b6ea36c1)

Actually, this was a workaround I found on the web for MSC,
but looking at the code I don't think it should work.
Probably, it has never been tested, so better remove it.

Now all the steps are guided

Now in the cppcheck plumed is not built or tested.
Only cppcheck is performed

@gtribello please check

This reverts commit e641cbb7.

(now I recall why I setted openmpi1.5: openmpi1.3 makes a regtest
fail randomly)

Changed flags for cppcheck so that it is optimized

I removed the NOPBC key from manual (it is not used)

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Detects the bug that was fixed in 68d501abd8ebabfa7131f74815c9917de3a56d92
(cherry picked from commit 87bf6d31)

This only affects transpose of non-square Tensors, that as
far as I know are never used in the code.
(cherry picked from commit ec5e599c)

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This is necessary if the MD program links a shared library

Addresses point 1 from issue #140

Point 2 is still unsolved and requires manual editing of cmake files.

(cherry picked from commit 2d9ac571)

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This fixes an issue on periodicity of values.

Now all the values are brought within their periodic boundaries.

I do it since an error in the last digit was making the
*next* commit fail. I first change the regtest to make it clear
that it is not changing