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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.

I think I made a mistake in a branch and overwrote the VERSION number

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evaluate gaussian was using always the periodicity of argument 0
plus some reorganisation of the code

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There was an issue when using
plumed vim2html --pdf --crop
on a plumed.dat file that is in a different directory.

(fixed by @a-cesari)

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This module was not actually maintained.

In case someone is interested in restoring it, contact the developers

After 7435705a
the correct "plumed_needs" keyword for molfile is "molfile_plugins"

Before:
- active modules were found based on on/off files.
- name of directory enclosing tests was used

After:
- active modules are found with "plumed config"
- modules are excluded explicitly in each rt/config file

Notice that crystallization/rt-urea needs two modules:
crystallization and adjmat

Actually I think the list of available modules in the Portfile
should be generated automatically

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It works creating a local Portfile so as to test
non released plumed versions.