Fix broken references in documentation

doc/Doxyfile.in

@@ -764,18 +764,18 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ./include/rapidjson/rapidjson.h \
-                         ./include/ \
-                         ./readme.md \
-                         ./doc/features.md \
-                         ./doc/tutorial.md \
-                         ./doc/stream.md \
-                         ./doc/encoding.md \
-                         ./doc/dom.md \
-                         ./doc/sax.md \
-                         ./doc/performance.md \
-                         ./doc/internals.md \
-                         ./doc/faq.md
+INPUT                  = readme.md \
+                         include/rapidjson/rapidjson.h \
+                         include/ \
+                         doc/features.md \
+                         doc/tutorial.md \
+                         doc/stream.md \
+                         doc/encoding.md \
+                         doc/dom.md \
+                         doc/sax.md \
+                         doc/performance.md \
+                         doc/internals.md \
+                         doc/faq.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
@@ -920,7 +920,7 @@ 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

doc/dom.md

@@ -31,7 +31,7 @@ User can customize these template parameters.
 
 ## Encoding {#Encoding}
 
-The `Encoding` parameter specifies the encoding of JSON String value in memory. Possible options are `UTF8`, `UTF16`, `UTF32`. Note that, these 3 types are also template class. `UTF8<>` is `UTF8<char>`, which means using char to store the characters. You may refer to [Encoding](encoding.md) for details.
+The `Encoding` parameter specifies the encoding of JSON String value in memory. Possible options are `UTF8`, `UTF16`, `UTF32`. Note that, these 3 types are also template class. `UTF8<>` is `UTF8<char>`, which means using char to store the characters. You may refer to [Encoding](doc/encoding.md) for details.
 
 Suppose a Windows application would query localization strings stored in JSON files. Unicode-enabled functions in Windows use UTF-16 (wide character) encoding. No matter what encoding was used in JSON files, we can store the strings in UTF-16 in memory.
 
@@ -106,7 +106,7 @@ GenericDocument& GenericDocument::Parse(const Ch* str);
 GenericDocument& GenericDocument::Parse(const Ch* str);
 ~~~~~~~~~~
 
-The examples of [tutorial](tutorial.md) uses (9) for normal parsing of string. The examples of [stream](stream.md) uses the first three. *In situ* parsing will be described soon.
+The examples of [tutorial](doc/tutorial.md) uses (9) for normal parsing of string. The examples of [stream](doc/stream.md) uses the first three. *In situ* parsing will be described soon.
 
 The `parseFlags` are combination of the following bit-flags:
 

doc/faq.md

@@ -4,7 +4,7 @@
 
 1. What is RapidJSON?
 
-   RapidJSON is a C++ library for parsing and generating JSON. You may check all [features](features.md) of it.
+   RapidJSON is a C++ library for parsing and generating JSON. You may check all [features](doc/features.md) of it.
 
 2. Why is it named so?
 

doc/tutorial.md

@@ -2,7 +2,7 @@
 
 This tutorial introduces the basics of the Document Object Model(DOM) API.
 
-As shown in [Usage at a glance](readme.md), a JSON can be parsed into DOM, and then the DOM can be queried and modified easily, and finally be converted back to JSON.
+As shown in [Usage at a glance](@ref index), a JSON can be parsed into DOM, and then the DOM can be queried and modified easily, and finally be converted back to JSON.
 
 [TOC]
 
@@ -512,4 +512,4 @@ This tutorial shows the basics of DOM tree query and manipulation. There are sev
 5. [Performance](doc/performance.md) shows some in-house and third-party benchmarks.
 6. [Internals](doc/internals.md) describes some internal designs and techniques of RapidJSON.
 
-You may also refer to the [FAQ](faq.md), API documentation, examples and unit tests.
+You may also refer to the [FAQ](doc/faq.md), API documentation, examples and unit tests.