While doing plumedcheck, verify that autoconf has been applied correctly

pushdoc script uses it to know if branches are supported or not

Merging debug flags and doc build (949397c0)
was a bad idea since the resulting job takes too long (doesn't
fit in 50 minutes for master branch)

I split them again, resulting in 6 jobs.

goes with a5daa52d

changed in order to work according to
e9aa6730

appliable -> applicable

failures are moved to the end of the list

(suggested by @valsson)

manual is always built. Developer doc has been updated accordingly
A total of 5 travis jobs is run each time

See #286

[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]