Have doxygen run in the doxygen directory

When the Doxywizzard GUI is used and the doxyfile is loaded, the
workind directory for doxygen is set to the location of the doxyfile.
However the Make and CMake build systems expect doxygen to be ran
from the top level directory.
This commit unifies the build system and the Doxywizzard GUI so that
all of them expect doxygen to be executed in the doxygen directory.
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3e47224..ca4cba2 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -126,8 +126,8 @@
 endif()
 
 ADD_CUSTOM_TARGET(apidoc
-    COMMAND doxygen doxygen/mbedtls.doxyfile
-    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+    COMMAND doxygen mbedtls.doxyfile
+    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doxygen)
 
 if(ENABLE_TESTING)
     enable_testing()
diff --git a/Makefile b/Makefile
index d475868..c1f6051 100644
--- a/Makefile
+++ b/Makefile
@@ -103,7 +103,7 @@
 
 apidoc:
 	mkdir -p apidoc
-	doxygen doxygen/mbedtls.doxyfile
+	cd doxygen; doxygen mbedtls.doxyfile
 
 apidoc_clean:
 	rm -rf apidoc
diff --git a/doxygen/mbedtls.doxyfile b/doxygen/mbedtls.doxyfile
index 5df1c93..0e148af 100644
--- a/doxygen/mbedtls.doxyfile
+++ b/doxygen/mbedtls.doxyfile
@@ -54,7 +54,7 @@
 # If a relative path is entered, it will be relative to the location
 # where doxygen was started. If left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = apidoc/
+OUTPUT_DIRECTORY       = ../apidoc/
 
 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
 # 4096 sub-directories (in 2 levels) under the output directory of each output
@@ -664,7 +664,7 @@
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = .
+INPUT                  = ..
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is