set doxygen so it can be run from the root dir

doc/doxygen.config

@@ -829,7 +829,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ../nuTens ../README.md
+INPUT                  = nuTens README.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1022,7 +1022,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE = ../README.md
+USE_MDFILE_AS_MAINPAGE = README.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
@@ -1151,7 +1151,7 @@ GENERATE_HTML          = YES
 # The default directory is: html.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_OUTPUT            = html
+HTML_OUTPUT            = doc/html
 
 # The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
 # generated HTML page (for example: .htm, .php, .asp).
@@ -1706,7 +1706,7 @@ GENERATE_LATEX         = YES
 # The default directory is: latex.
 # This tag requires that the tag GENERATE_LATEX is set to YES.
 
-LATEX_OUTPUT           = latex
+LATEX_OUTPUT           = doc/latex
 
 # The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
 # invoked.