Fixed documentation generation for Doxygen 1.13.

Set IMPLICIT_DIR_DOCS to NO to fix references to .md files. Also strip
common paths so the file list starts at the module-specific folder within
the include folder.

doc/CMakeLists.txt

@@ -4,6 +4,8 @@ endif()
 
 set(docSource "\"${DEEPSEA_SOURCE_DIR}/README.md\"")
 set(dependencies ${DEEPSEA_SOURCE_DIR}/README.md)
+set(includeDirs)
+set(strippedPrefixes "\"${DEEPSEA_SOURCE_DIR}\"")
 get_property(modules GLOBAL PROPERTY DEEPSEA_MODULE_PATHS)
 foreach (docProject ${modules})
 	set(thisDir ${DEEPSEA_MODULE_DIR}/${docProject})
@@ -14,6 +16,7 @@ foreach (docProject ${modules})
 	endforeach()
 	set(docSource "${docSource} \"${thisDir}/include\" ${quotedMDFiles}")
 	set(includeDirs "${includeDirs} \"${thisDir}/include\"")
+	set(strippedPrefixes "${strippedPrefixes} \"${thisDir}/include/DeepSea\"")
 	file(GLOB_RECURSE theseDependencies ${thisDir}/include/*.h)
 	set(dependencies ${dependencies} ${theseDependencies} ${mdFiles})
 endforeach()

doc/Doxyfile.in

@@ -162,7 +162,7 @@ FULL_PATH_NAMES        = YES
 # will be relative from the directory where doxygen is started.
 # This tag requires that the tag FULL_PATH_NAMES is set to YES.
 
-STRIP_FROM_PATH        = @sourceDirs@
+STRIP_FROM_PATH        = @strippedPrefixes@
 
 # The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
 # path mentioned in the documentation of a class, which tells the reader which
@@ -968,6 +968,14 @@ FILTER_SOURCE_PATTERNS =
 
 USE_MDFILE_AS_MAINPAGE = @DEEPSEA_SOURCE_DIR@/README.md
 
+# If the IMPLICIT_DIR_DOCS tag is set to YES, any README.md file found in
+# sub-directories of the project's root, is used as the documentation for that
+# sub-directory, except when the README.md starts with a \dir, \page or
+# \mainpage command. If set to NO, the README.md file needs to start with an
+# explicit \dir command in order to be used as directory documentation.
+
+IMPLICIT_DIR_DOCS      = NO
+
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
 #---------------------------------------------------------------------------