title: doxygen is not searching the include directory
body: <p>Sorry about the length of this post.  I am using <em>Doxygen 1.8.10</em> on a <em>W7 64</em> bit machine. I have written and compiled my code in code::blocks 13.12.</p>
  
  <p>My file structure is as follows: <code>D:/Base/CodeBlocksProjects/SFML_apps/Alarm Clock</code> contains my <code>cpp</code> files and all my header files are in <code>/CodeBlocksProjects/include</code>.      </p>
  
  <p>I want the Doxygen documentation to be saved in <code>/CodeBlocksProjects/SFML_apps/Alarm Clock/Doxygen</code>. This is set as the working directory. 
  <code>OUTPUT_DIRECTORY</code> is set to <code>.</code> (a single dot). This means as I understand it that Doxygen will save it's generated files in <code>/Alarm Clock/Doxygen</code>.<br>
  INPUT is set to <code>../</code> which should mean Doxygen will look for source files in <code>/Alarm Clock/</code> folder.  <code>SEARCH_INCLUDES</code> is on and the include path is <code>../../../include</code>. This relative path is generated when I use the directory finder button to point to my include folder.  </p>
  
  <p>Everything else is pretty much to the defaults. But my include files are not being found and listed so there is no class information except for a few trivial classes that are in various test files in the <code>/Alarm Clock/</code> folder.
  I have appended the Doxyfile settings.  </p>
  
  <p>Any help would be much appreciated. I have completed this code and I want to document it before moving on ...    </p>
  
  <pre><code># Doxyfile 1.8.10    
  
  #---------------------------------------------------------------------------    
  # Project related configuration options    
  #---------------------------------------------------------------------------    
  DOXYFILE_ENCODING      = UTF-8    
  PROJECT_NAME           = "Alarm Clock"    
  PROJECT_NUMBER         = "Beta 1.01"    
  PROJECT_BRIEF          =     
  PROJECT_LOGO           =     
  OUTPUT_DIRECTORY       = .    
  CREATE_SUBDIRS         = NO    
  ALLOW_UNICODE_NAMES    = NO    
  OUTPUT_LANGUAGE        = English    
  BRIEF_MEMBER_DESC      = YES    
  REPEAT_BRIEF           = YES    
  ABBREVIATE_BRIEF       =     
  ALWAYS_DETAILED_SEC    = NO    
  INLINE_INHERITED_MEMB  = NO    
  FULL_PATH_NAMES        = NO    
  STRIP_FROM_PATH        =     
  STRIP_FROM_INC_PATH    =     
  SHORT_NAMES            = NO    
  JAVADOC_AUTOBRIEF      = NO    
  QT_AUTOBRIEF           = NO    
  MULTILINE_CPP_IS_BRIEF = NO    
  INHERIT_DOCS           = YES    
  SEPARATE_MEMBER_PAGES  = NO    
  TAB_SIZE               = 8    
  ALIASES                =     
  TCL_SUBST              =     
  OPTIMIZE_OUTPUT_FOR_C  = NO    
  OPTIMIZE_OUTPUT_JAVA   = NO    
  OPTIMIZE_FOR_FORTRAN   = NO    
  OPTIMIZE_OUTPUT_VHDL   = NO    
  EXTENSION_MAPPING      =     
  MARKDOWN_SUPPORT       = YES    
  AUTOLINK_SUPPORT       = YES    
  BUILTIN_STL_SUPPORT    = NO    
  CPP_CLI_SUPPORT        = NO    
  SIP_SUPPORT            = NO    
  IDL_PROPERTY_SUPPORT   = YES    
  DISTRIBUTE_GROUP_DOC   = NO    
  GROUP_NESTED_COMPOUNDS = NO    
  SUBGROUPING            = YES    
  INLINE_GROUPED_CLASSES = NO    
  INLINE_SIMPLE_STRUCTS  = NO    
  TYPEDEF_HIDES_STRUCT   = NO    
  LOOKUP_CACHE_SIZE      = 0    
  #---------------------------------------------------------------------------    
  # Build related configuration options    
  #---------------------------------------------------------------------------    
  EXTRACT_ALL            = YES    
  EXTRACT_PRIVATE        = YES    
  EXTRACT_PACKAGE        = YES    
  EXTRACT_STATIC         = YES    
  EXTRACT_LOCAL_CLASSES  = YES    
  EXTRACT_LOCAL_METHODS  = NO    
  EXTRACT_ANON_NSPACES   = NO    
  HIDE_UNDOC_MEMBERS     = NO    
  HIDE_UNDOC_CLASSES     = NO    
  HIDE_FRIEND_COMPOUNDS  = NO    
  HIDE_IN_BODY_DOCS      = NO    
  INTERNAL_DOCS          = NO    
  CASE_SENSE_NAMES       = NO    
  HIDE_SCOPE_NAMES       = NO    
  HIDE_COMPOUND_REFERENCE= NO    
  SHOW_INCLUDE_FILES     = YES    
  SHOW_GROUPED_MEMB_INC  = NO    
  FORCE_LOCAL_INCLUDES   = YES    
  INLINE_INFO            = YES    
  SORT_MEMBER_DOCS       = YES    
  SORT_BRIEF_DOCS        = NO    
  SORT_MEMBERS_CTORS_1ST = NO    
  SORT_GROUP_NAMES       = NO    
  SORT_BY_SCOPE_NAME     = NO    
  STRICT_PROTO_MATCHING  = NO    
  GENERATE_TODOLIST      = YES    
  GENERATE_TESTLIST      = YES    
  GENERATE_BUGLIST       = YES    
  GENERATE_DEPRECATEDLIST= YES    
  ENABLED_SECTIONS       =     
  MAX_INITIALIZER_LINES  = 30    
  SHOW_USED_FILES        = YES    
  SHOW_FILES             = YES    
  SHOW_NAMESPACES        = YES    
  FILE_VERSION_FILTER    =     
  LAYOUT_FILE            =     
  CITE_BIB_FILES         =     
  #---------------------------------------------------------------------------    
  # Configuration options related to warning and progress messages    
  #---------------------------------------------------------------------------    
  QUIET                  = NO    
  WARNINGS               = YES    
  WARN_IF_UNDOCUMENTED   = NO    
  WARN_IF_DOC_ERROR      = YES    
  WARN_NO_PARAMDOC       = YES    
  WARN_FORMAT            = "$file:$line: $text"    
  WARN_LOGFILE           = "D:\Coding\CodeBlocksProjects\SFML_Apps\Alarm Clock\doxygen\doxygen.log"    
  #---------------------------------------------------------------------------    
  # Configuration options related to the input files    
  #---------------------------------------------------------------------------    
  INPUT                  = ../    
  INPUT_ENCODING         = UTF-8    
  FILE_PATTERNS          =     
  RECURSIVE              = YES    
  EXCLUDE                =     
  EXCLUDE_SYMLINKS       = NO    
  EXCLUDE_PATTERNS       =     
  EXCLUDE_SYMBOLS        =     
  EXAMPLE_PATH           =     
  EXAMPLE_PATTERNS       =     
  EXAMPLE_RECURSIVE      = NO    
  IMAGE_PATH             =     
  INPUT_FILTER           =     
  FILTER_PATTERNS        =     
  FILTER_SOURCE_FILES    = NO    
  FILTER_SOURCE_PATTERNS =     
  USE_MDFILE_AS_MAINPAGE =     
  #---------------------------------------------------------------------------    
  # Configuration options related to source browsing    
  #---------------------------------------------------------------------------    
  SOURCE_BROWSER         = YES    
  INLINE_SOURCES         = YES    
  STRIP_CODE_COMMENTS    = YES    
  REFERENCED_BY_RELATION = YES    
  REFERENCES_RELATION    = YES    
  REFERENCES_LINK_SOURCE = YES    
  SOURCE_TOOLTIPS        = YES    
  USE_HTAGS              = NO    
  VERBATIM_HEADERS       = YES    
  #---------------------------------------------------------------------------    
  # Configuration options related to the alphabetical class index    
  #---------------------------------------------------------------------------    
  ALPHABETICAL_INDEX     = YES    
  COLS_IN_ALPHA_INDEX    = 5    
  IGNORE_PREFIX          =     
  #---------------------------------------------------------------------------    
  # Configuration options related to the HTML output    
  #---------------------------------------------------------------------------    
  GENERATE_HTML          = YES    
  HTML_OUTPUT            = html    
  HTML_FILE_EXTENSION    = .html    
  HTML_HEADER            =     
  HTML_FOOTER            =     
  HTML_STYLESHEET        =     
  HTML_EXTRA_STYLESHEET  =     
  HTML_EXTRA_FILES       =     
  HTML_COLORSTYLE_HUE    = 220    
  HTML_COLORSTYLE_SAT    = 100    
  HTML_COLORSTYLE_GAMMA  = 80    
  HTML_TIMESTAMP         = YES    
  HTML_DYNAMIC_SECTIONS  = NO    
  HTML_INDEX_NUM_ENTRIES = 100    
  GENERATE_DOCSET        = NO    
  DOCSET_FEEDNAME        = "Doxygen generated docs"    
  DOCSET_BUNDLE_ID       = org.doxygen.Project    
  DOCSET_PUBLISHER_ID    = org.doxygen.Publisher    
  DOCSET_PUBLISHER_NAME  = Publisher    
  GENERATE_HTMLHELP      = NO    
  CHM_FILE               = "../Alarm Clock.chm"    
  HHC_LOCATION           =     
  GENERATE_CHI           = NO    
  CHM_INDEX_ENCODING     =     
  BINARY_TOC             = NO    
  TOC_EXPAND             = NO    
  GENERATE_QHP           = NO    
  QCH_FILE               =     
  QHP_NAMESPACE          = org.doxygen.Project    
  QHP_VIRTUAL_FOLDER     = doc    
  QHP_CUST_FILTER_NAME   =     
  QHP_CUST_FILTER_ATTRS  =     
  QHP_SECT_FILTER_ATTRS  =     
  QHG_LOCATION           =     
  GENERATE_ECLIPSEHELP   = NO    
  ECLIPSE_DOC_ID         = org.doxygen.Project    
  DISABLE_INDEX          = NO    
  GENERATE_TREEVIEW      = YES    
  ENUM_VALUES_PER_LINE   = 4    
  TREEVIEW_WIDTH         = 250    
  EXT_LINKS_IN_WINDOW    = NO    
  FORMULA_FONTSIZE       = 10    
  FORMULA_TRANSPARENT    = YES    
  USE_MATHJAX            = NO    
  MATHJAX_FORMAT         = HTML-CSS    
  MATHJAX_RELPATH        = http://www.mathjax.org/mathjax    
  MATHJAX_EXTENSIONS     =     
  MATHJAX_CODEFILE       =     
  SEARCHENGINE           = YES    
  SERVER_BASED_SEARCH    = NO    
  EXTERNAL_SEARCH        = NO    
  SEARCHENGINE_URL       =     
  SEARCHDATA_FILE        = searchdata.xml    
  EXTERNAL_SEARCH_ID     =     
  EXTRA_SEARCH_MAPPINGS  =     
  #---------------------------------------------------------------------------    
  # Configuration options related to the LaTeX output    
  #---------------------------------------------------------------------------    
  GENERATE_LATEX         = NO    
  LATEX_OUTPUT           = latex    
  LATEX_CMD_NAME         = latex    
  MAKEINDEX_CMD_NAME     = makeindex    
  COMPACT_LATEX          = NO    
  PAPER_TYPE             = a4    
  EXTRA_PACKAGES         =     
  LATEX_HEADER           =     
  LATEX_FOOTER           =     
  LATEX_EXTRA_STYLESHEET =     
  LATEX_EXTRA_FILES      =     
  PDF_HYPERLINKS         = YES    
  USE_PDFLATEX           = YES    
  LATEX_BATCHMODE        = NO    
  LATEX_HIDE_INDICES     = NO    
  LATEX_SOURCE_CODE      = NO    
  LATEX_BIB_STYLE        = plain    
  #---------------------------------------------------------------------------    
  # Configuration options related to the RTF output    
  #---------------------------------------------------------------------------    
  GENERATE_RTF           = YES    
  RTF_OUTPUT             = rtf    
  COMPACT_RTF            = NO    
  RTF_HYPERLINKS         = NO    
  RTF_STYLESHEET_FILE    =     
  RTF_EXTENSIONS_FILE    =     
  RTF_SOURCE_CODE        = NO    
  #---------------------------------------------------------------------------    
  # Configuration options related to the man page output    
  #---------------------------------------------------------------------------    
  GENERATE_MAN           = NO    
  MAN_OUTPUT             = man    
  MAN_EXTENSION          = .3    
  MAN_SUBDIR             =     
  MAN_LINKS              = NO    
  #---------------------------------------------------------------------------    
  # Configuration options related to the XML output    
  #---------------------------------------------------------------------------    
  GENERATE_XML           = NO    
  XML_OUTPUT             = xml    
  XML_PROGRAMLISTING     = YES    
  #---------------------------------------------------------------------------    
  # Configuration options related to the DOCBOOK output    
  #---------------------------------------------------------------------------    
  GENERATE_DOCBOOK       = NO    
  DOCBOOK_OUTPUT         = docbook    
  DOCBOOK_PROGRAMLISTING = NO    
  #---------------------------------------------------------------------------    
  # Configuration options for the AutoGen Definitions output    
  #---------------------------------------------------------------------------    
  GENERATE_AUTOGEN_DEF   = NO    
  #---------------------------------------------------------------------------    
  # Configuration options related to the Perl module output    
  #---------------------------------------------------------------------------    
  GENERATE_PERLMOD       = NO    
  PERLMOD_LATEX          = NO    
  PERLMOD_PRETTY         = YES    
  PERLMOD_MAKEVAR_PREFIX =     
  #---------------------------------------------------------------------------    
  # Configuration options related to the preprocessor    
  #---------------------------------------------------------------------------    
  ENABLE_PREPROCESSING   = YES    
  MACRO_EXPANSION        = YES    
  EXPAND_ONLY_PREDEF     = NO    
  SEARCH_INCLUDES        = YES    
  INCLUDE_PATH           = ../../../include    
  INCLUDE_FILE_PATTERNS  =     
  PREDEFINED             =     
  EXPAND_AS_DEFINED      =     
  SKIP_FUNCTION_MACROS   = NO    
  #---------------------------------------------------------------------------    
  # Configuration options related to external references    
  #---------------------------------------------------------------------------    
  TAGFILES               =     
  GENERATE_TAGFILE       =     
  ALLEXTERNALS           = NO    
  EXTERNAL_GROUPS        = YES    
  EXTERNAL_PAGES         = YES    
  PERL_PATH              = /usr/bin/perl    
  #---------------------------------------------------------------------------    
  # Configuration options related to the dot tool    
  #---------------------------------------------------------------------------    
  CLASS_DIAGRAMS         = YES    
  MSCGEN_PATH            =     
  DIA_PATH               =     
  HIDE_UNDOC_RELATIONS   = YES    
  HAVE_DOT               = YES    
  DOT_NUM_THREADS        = 0    
  DOT_FONTNAME           = Helvetica    
  DOT_FONTSIZE           = 10    
  DOT_FONTPATH           =     
  CLASS_GRAPH            = YES    
  COLLABORATION_GRAPH    = YES    
  GROUP_GRAPHS           = YES    
  UML_LOOK               = NO    
  UML_LIMIT_NUM_FIELDS   = 10    
  TEMPLATE_RELATIONS     = NO    
  INCLUDE_GRAPH          = YES    
  INCLUDED_BY_GRAPH      = YES    
  CALL_GRAPH             = YES    
  CALLER_GRAPH           = YES    
  GRAPHICAL_HIERARCHY    = YES    
  DIRECTORY_GRAPH        = YES    
  DOT_IMAGE_FORMAT       = png    
  INTERACTIVE_SVG        = NO    
  DOT_PATH               = "C:\Program Files (x86)\Graphviz2.38\bin\dot.exe"    
  DOTFILE_DIRS           =     
  MSCFILE_DIRS           =     
  DIAFILE_DIRS           =     
  PLANTUML_JAR_PATH      =     
  PLANTUML_INCLUDE_PATH  =     
  DOT_GRAPH_MAX_NODES    = 50    
  MAX_DOT_GRAPH_DEPTH    = 0    
  DOT_TRANSPARENT        = NO    
  DOT_MULTI_TARGETS      = NO    
  GENERATE_LEGEND        = YES    
  DOT_CLEANUP            = YES  
  </code></pre>