diff --git a/docs/doxygen.cfg b/docs/doxygen.cfg
index fb2b859b976..9627f8c3c3a 100644
--- a/docs/doxygen.cfg
+++ b/docs/doxygen.cfg
@@ -302,7 +302,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories 
 # with spaces.
 
-INPUT                  = ..
+INPUT                  = ../..
 
 # If the value of the INPUT tag contains directories, you can use the 
 # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
@@ -323,7 +323,7 @@ RECURSIVE              = YES
 # excluded from the INPUT source files. This way you can easily exclude a 
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
 
-EXCLUDE                =  ../test ../include/boost
+EXCLUDE                =  ../../test ../../include/boost
 
 # If the value of the INPUT tag contains directories, you can use the 
 # EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude 
@@ -697,7 +697,7 @@ SEARCH_INCLUDES        = YES
 # contain include files that are not input files but should be processed by 
 # the preprocessor.
 
-INCLUDE_PATH           = ../include
+INCLUDE_PATH           = ../../include
 
 # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard 
 # patterns (like *.h and *.hpp) to filter out the header-files in the 
diff --git a/docs/doxygen.cfg.in b/docs/doxygen.cfg.in
index fb2b859b976..9627f8c3c3a 100644
--- a/docs/doxygen.cfg.in
+++ b/docs/doxygen.cfg.in
@@ -302,7 +302,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories 
 # with spaces.
 
-INPUT                  = ..
+INPUT                  = ../..
 
 # If the value of the INPUT tag contains directories, you can use the 
 # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp 
@@ -323,7 +323,7 @@ RECURSIVE              = YES
 # excluded from the INPUT source files. This way you can easily exclude a 
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
 
-EXCLUDE                =  ../test ../include/boost
+EXCLUDE                =  ../../test ../../include/boost
 
 # If the value of the INPUT tag contains directories, you can use the 
 # EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude 
@@ -697,7 +697,7 @@ SEARCH_INCLUDES        = YES
 # contain include files that are not input files but should be processed by 
 # the preprocessor.
 
-INCLUDE_PATH           = ../include
+INCLUDE_PATH           = ../../include
 
 # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard 
 # patterns (like *.h and *.hpp) to filter out the header-files in the