doc: Improve Doxygen target and update Doxyfile

# Doxygen target to generate API reference #

############################################

SET(DOCS_DOXYGEN_BINARY_DIR "${CMAKE_CURRENT_BINARY_DIR}/reference")

FIND_PACKAGE(Doxygen)

IF(DOXYGEN_FOUND)

    CONFIGURE_FILE(${PROJECT_SOURCE_DIR}/doc/reference/Doxyfile.in ${CMAKE_BINARY_DIR}/reference/Doxyfile @ONLY)

CONFIGURE_FILE("${CMAKE_CURRENT_SOURCE_DIR}/reference/Doxyfile" "${DOCS_DOXYGEN_BINARY_DIR}/Doxyfile" @ONLY)

ADD_CUSTOM_TARGET(

        ${CMAKE_PROJECT_NAME}-reference

        ${DOXYGEN_EXECUTABLE} ${CMAKE_BINARY_DIR}/reference/Doxyfile

        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/reference

        COMMENT "Generating API documentation with Doxygen"

    apsq_docs_reference

    COMMAND Doxygen::doxygen "${DOCS_DOXYGEN_BINARY_DIR}/Doxyfile"

    DEPENDS Doxygen::doxygen

    WORKING_DIRECTORY "${DOCS_DOXYGEN_BINARY_DIR}"

    COMMENT "Generating API reference with Doxygen"

    VERBATIM)

ENDIF(DOXYGEN_FOUND)

#######################################

# Target to create Markdown file tree #