[makedoc]

Added in the list of options to be tested:
$($CXX --print-prog-name=ld) -r -o
As suggested by @alalazo

Since this option appears to work also with old compilers, I try
it as a first option.

See #291

Spot out by cppcheck on master branch. Since the problem is relevant
also for v2.3, I fix it here.

This command should be more portable. Notice that with old
gcc (e.g. 4.6) this does not work. I added a test such that
when this does not work "ld -r -o" is tried instead

removed extra comma

This change allows to load libraries locate in src/lib more easily
on a mac. Notice that traditionally this was solved by setting
DYLD_LIBRARY_PATH. However, as of osx Capitan, DYLD_LIBRARY_PATH
does not work correctly. Fixing the installed path with
install_name_tool should solve the issue.

(backported from master)

after 18b63365

instead of looking for last commit, sort them by year

Thanks to @valsson

Related to fb70153e

Small typo in the regtests log

[makedoc]

[makedoc]

When using --disable-libsearch, external molfile_plugins were unconditionally
disabled. Fixed now.

[makedoc]

manual: removed some incompleted and duplicated documentation from group.txt and expanded a bit that in MOLINFO
[makedoc]

close #263

[makedoc]

[makedoc]

Regenerated after c40b96fe

Only detect renames with identity > 75%. This allows a more
precise indication of the year when a file appeared in the repository,
that is used to generate headers.

(thanks to Pratyush Tiwary)

[makedoc]

See #247

[makedoc]

[makedoc]

it has some problem with travis-ci

(no impact on plumed src)

[makedoc]

Since matheval evaluator is not thread safe, it is necessary to allocate
one evaluator per threads

Closes #249

These tests were marked as needing matheval incorrectly

[makedoc]

After d669afb2 there was still
a fix in EffectiveEnergyDrift.cpp when a domain had zero atoms.

This could affect real calculations, so I think this fix should be
backported to v2.3

Fixes #246

(cherry picked from commit 97d7c422)

There was a bug in driver with --debug-pd when, unluckily, the
last domain had by chance zero atoms

(cherry picked from commit d669afb2)