I replaced a few pointers with vectors or arrays

brought the "changes after alpha" up together with other changes

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.

[makedoc]

Three versions are installed:
plumed - flags to link plumed (as in patch --shared)
plumedWrapper - flag to link plumed wrapper only (as in patch --runtime)
plumedInternals - flags to link full plumed library, including required CPPFLAGS

Notice that some macros are stripped from CPPFLAGS. This might
be improved in order to keep only the relevant ones.

This library contains only the wrapper/Plumed.o object and
can be used to link plumed with --runtime option without
incurring in linking errors when the MD code links PLUMED_LOAD
variables more than ones

Grid: function to reset to default %14.9f output format

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