Move generation of documentation files out from the source tree

Documentation will now be built in the directory from which cmake was
invoked. Doxyfile.in updated and Doxyfile.generic (unused) has been
removed. In-tree generation was causing problems in some environments
and IDEs (such as CLion)

CMakeLists.txt

@@ -844,7 +844,7 @@ find_package(Doxygen)
 if(DOXYGEN_FOUND)
      message(STATUS "Doxygen found.")
      message(STATUS "You can build the documentation with 'make doc'." )
-     message(STATUS "When done, point your browser to ${CMAKE_SOURCE_DIR}/html/index.html")
+     message(STATUS "When done, point your browser to ${CMAKE_BINARY_DIR}/html/index.html")
      set(HAVE_DOT ${DOXYGEN_DOT_FOUND})
      file(TO_NATIVE_PATH ${CMAKE_SOURCE_DIR} top_srcdir)
      file(TO_NATIVE_PATH ${CMAKE_BINARY_DIR} top_builddir)
@@ -857,30 +857,30 @@ if(DOXYGEN_FOUND)
           set(GNSSSDR_USE_MATHJAX "YES")
      endif(PDFLATEX_COMPILER)
      configure_file(${CMAKE_SOURCE_DIR}/docs/doxygen/Doxyfile.in
-          ${CMAKE_SOURCE_DIR}/docs/doxygen/Doxyfile
+          ${CMAKE_BINARY_DIR}/docs/doxygen/Doxyfile
           @ONLY
      )
      add_custom_target(doc
-          ${DOXYGEN_EXECUTABLE} ${CMAKE_SOURCE_DIR}/docs/doxygen/Doxyfile
-          WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+          ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/docs/doxygen/Doxyfile
+          WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
           COMMENT "Generating API documentation with Doxygen." VERBATIM
      )
      if(LATEX_COMPILER)
-          message(STATUS "'make pdfmanual' will generate a manual at ${CMAKE_SOURCE_DIR}/docs/GNSS-SDR_manual.pdf")
+          message(STATUS "'make pdfmanual' will generate a manual at ${CMAKE_BINARY_DIR}/docs/GNSS-SDR_manual.pdf")
           add_custom_target(pdfmanual
                COMMAND ${CMAKE_MAKE_PROGRAM}
-               COMMAND ${CMAKE_COMMAND} -E copy refman.pdf ${CMAKE_SOURCE_DIR}/docs/GNSS-SDR_manual.pdf
+               COMMAND ${CMAKE_COMMAND} -E copy refman.pdf ${CMAKE_BINARY_DIR}/docs/GNSS-SDR_manual.pdf
                COMMAND ${CMAKE_MAKE_PROGRAM} clean
                DEPENDS doc
-               WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/docs/latex
+               WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/docs/latex
                COMMENT "Generating PDF manual with Doxygen." VERBATIM
           )
      endif(LATEX_COMPILER)
      message(STATUS "'make doc-clean' will clean the documentation.")
      add_custom_target(doc-clean
-          COMMAND ${CMAKE_COMMAND} -E remove_directory ${CMAKE_SOURCE_DIR}/docs/html
-          COMMAND ${CMAKE_COMMAND} -E remove_directory ${CMAKE_SOURCE_DIR}/docs/latex
-          COMMAND ${CMAKE_COMMAND} -E remove ${CMAKE_SOURCE_DIR}/docs/GNSS-SDR_manual.pdf
+          COMMAND ${CMAKE_COMMAND} -E remove_directory ${CMAKE_BINARY_DIR}/docs/html
+          COMMAND ${CMAKE_COMMAND} -E remove_directory ${CMAKE_BINARY_DIR}/docs/latex
+          COMMAND ${CMAKE_COMMAND} -E remove ${CMAKE_BINARY_DIR}/docs/GNSS-SDR_manual.pdf
           COMMENT "Cleaning documentation." VERBATIM
      )
 else(DOXYGEN_FOUND)

README.md

@@ -226,14 +226,14 @@ You could be interested in creating the documentation by doing:
 $ make doc
 ~~~~~~ 
 
-from the gnss-sdr/build folder. This will generate HTML documentation that can be retrieved pointing your browser of preference to gnss-sdr/docs/html/index.html.
+from the gnss-sdr/build folder. This will generate HTML documentation that can be retrieved pointing your browser of preference to build/docs/html/index.html.
 If a LaTeX installation is detected in your system,
 
 ~~~~~~ 
 $ make pdfmanual
 ~~~~~~ 
 
-will create a PDF manual at gnss-sdr/docs/GNSS-SDR_manual.pdf. Finally,
+will create a PDF manual at build/docs/GNSS-SDR_manual.pdf. Finally,
 
 ~~~~~~ 
 $ make doc-clean
@@ -453,7 +453,7 @@ $ make doc
 and can be viewed doing:
 
 ~~~~~~ 
-$ open ../docs/html/index.html
+$ open ./docs/html/index.html
 ~~~~~~ 
 
 GNSS-SDR comes with a library which is a module of the Vector-Optimized Library of Kernels (so called [VOLK_GNSSSDR](./src/algorithms/libs/volk_gnsssdr_module/volk_gnsssdr/README.md)) and a profiler that will build a config file for the best SIMD architecture for your processor. Run ```volk_gnsssdr_profile``` that is installed into ```$PREFIX/bin```. This program tests all known VOLK kernels for each architecture supported by the processor. When finished, it will write to ```$HOME/.volk_gnsssdr/volk_gnsssdr_config``` the best architecture for the VOLK function. This file is read when using a function to know the best version of the function to execute. It mimics GNU Radio's [VOLK](http://libvolk.org/) library, so if you still have not run ```volk_profile```, this is a good moment to do so.