Tuned travis file

I changed a few things:
1. instead of checking with "--enable-debug" and "--enable-debug --enable-debug-glibcxx"
  I always use both.
2. I check with debug flags and serial compiler (before it was only debug+MPI)
3. I changed the order so that runs with manual is the first and runs
  with debug options are also made earlier. This is convenient since they
  take more time

.travis.yml

 language: cpp
 env:
 # list of configurations to be attempted:
-# clang
+# MPI + doc
+# this is the "master" one, it is going to update the manual if log contains [makedoc]
+  - PLUMED_CC=mpicc PLUMED_CXX=mpic++ MAKEDOC=yes ALMOST=yes
+# the following two are with debug flags, including bound check
+# I think clang does not support debug-glibcxx, so I skip it here
+  - PLUMED_CC=gcc   PLUMED_CXX=g++    CONFIG_FLAGS="--enable-debug --enable-debug-glibcxx"
+  - PLUMED_CC=mpicc PLUMED_CXX=mpic++ CONFIG_FLAGS="--enable-debug --enable-debug-glibcxx"
+# then I try serial compilers
   - PLUMED_CC=clang PLUMED_CXX=clang++
-# GNU
   - PLUMED_CC=gcc   PLUMED_CXX=g++
-# MPI + doc
-  - PLUMED_CC=mpicc PLUMED_CXX=mpic++ MAKEDOC=yes
-# clang
+# then check with different optimization flags
   - PLUMED_CC=clang PLUMED_CXX=clang++ PLUMED_CXXFLAGS=-O3 LAPACK=yes
-# GNU
   - PLUMED_CC=gcc   PLUMED_CXX=g++     PLUMED_CXXFLAGS=-O3 LAPACK=yes
-# MPI
-  - PLUMED_CC=mpicc PLUMED_CXX=mpic++  PLUMED_CXXFLAGS=-O3 LAPACK=yes ALMOST=yes
-# MPI + debug
-  - PLUMED_CC=mpicc PLUMED_CXX=mpic++  CONFIG_FLAGS=--enable-debug
-# MPI + bound check (could be very slow)
-  - PLUMED_CC=mpicc PLUMED_CXX=mpic++  CONFIG_FLAGS="--enable-debug --enable-debug-glibcxx"
+  - PLUMED_CC=mpicc PLUMED_CXX=mpic++  PLUMED_CXXFLAGS=-O3 LAPACK=yes
 # Possible additional variables:
 #   VALGRIND=yes to make valgrind tests, only when log contains string [valgrind]
 install: