Update README.md and CHANGELOG.md

Author: robertodr

CHANGELOG.md

@@ -46,8 +46,6 @@
 - Switched to the latest version of
   [Autocmake](http://autocmake.readthedocs.io/) The configuration file is now YAML-based.
   The PyYAML module is thus required.
-- The standalone `run_pcm` executable now uses the API functions instead of the
-  internal headers.
 - The extended diagnostic flags `-Wsuggest-attribute=pure
   -Wsuggest-attribute=const -Wsuggest-attribute=noreturn -Wsuggest-final-types
   -Wsuggest-final-methods -Wsuggest-override -Wuseless-cast
@@ -56,6 +54,11 @@
 - The C++11 compatibility CMake macros now check for the availability of the
   `noreturn` attribute. A workaround macro, accessible _via_ `__noreturn`, has
   been added to the `Cxx11Workarounds.hpp` header file.
+- **BREAKING CHANGE** The ouput flushing function must be passed explicitly as
+  a function pointer to the `pcmsolver_new` function during library
+  initialization.
+  The function pointer has the signature `typedef void (*HostWriter)(const char
+  * message)` thus accepting a single argument instead of the previous two.
 
 ### Deprecated
 

README.md

@@ -11,13 +11,13 @@ PCMSolver
 An API for the Polarizable Continuum Model.
 
 - [Project website](https://gitlab.com/PCMSolver/pcmsolver)
-- [Changelog](../master/CHANGELOG.md)
-- [Documentation](http://pcmsolver.readthedocs.org)
+- [Changelog](CHANGELOG.md)
+- [Documentation](http://pcmsolver.readthedocs.io)
 - [Build and test history](https://travis-ci.org/PCMSolver/pcmsolver/builds)
 - [Nightly build dashboard](https://testboard.org/cdash/index.php?project=PCMSolver)
 - Version 1.1.6 available
-- Licensed under [LGPLv3](../master/LICENSE)
-- CMake infrastructure managed *via* [Autocmake](http://autocmake.readthedocs.org/)
+- Licensed under [LGPLv3](LICENSE)
+- CMake infrastructure managed *via* [Autocmake](http://autocmake.readthedocs.io/)
 
 Primary test environments
 =========================

src/bin/run_pcm.cpp

@@ -65,7 +65,7 @@ int main(int argc, char * argv[]) {
   pcmsolver_out.open(remove_extension(argv[1]).erase(0, 1) + ".out");
   context_.printInfo();
 
-  size_t size = context_.getCavitySize();
+  PCMSolverIndex size = context_.getCavitySize();
 
   // Form vector with electrostatic potential
   // First compute the potential from the classical point multipoles distribution