diff --git a/hadoop-common-project/hadoop-auth/src/site/apt/Configuration.apt.vm b/hadoop-common-project/hadoop-auth/src/site/apt/Configuration.apt.vm
index f2fe11d8f6..61bd857515 100644
--- a/hadoop-common-project/hadoop-auth/src/site/apt/Configuration.apt.vm
+++ b/hadoop-common-project/hadoop-auth/src/site/apt/Configuration.apt.vm
@@ -24,8 +24,7 @@ Configuration
 
 * Server Side Configuration Setup
 
-  The {{{./apidocs/org/apache/hadoop/auth/server/AuthenticationFilter.html}
-  AuthenticationFilter filter}} is Hadoop Auth's server side component.
+  The AuthenticationFilter filter is Hadoop Auth's server side component.
 
   This filter must be configured in front of all the web application resources
   that required authenticated requests. For example:
@@ -46,9 +45,7 @@ Configuration
     must start with the prefix. The default value is no prefix.
 
   * <<<[PREFIX.]type>>>: the authentication type keyword (<<<simple>>> or
-    <<<kerberos>>>) or a
-    {{{./apidocs/org/apache/hadoop/auth/server/AuthenticationHandler.html}
-    Authentication handler implementation}}.
+    <<<kerberos>>>) or a Authentication handler implementation.
 
   * <<<[PREFIX.]signature.secret>>>: The secret to SHA-sign the generated
     authentication tokens. If a secret is not provided a random secret is
diff --git a/hadoop-common-project/hadoop-auth/src/site/apt/index.apt.vm b/hadoop-common-project/hadoop-auth/src/site/apt/index.apt.vm
index 26fc2492ca..6051f8cbf2 100644
--- a/hadoop-common-project/hadoop-auth/src/site/apt/index.apt.vm
+++ b/hadoop-common-project/hadoop-auth/src/site/apt/index.apt.vm
@@ -52,7 +52,3 @@ Hadoop Auth, Java HTTP SPNEGO ${project.version}
 
   * {{{./BuildingIt.html}Building It}}
 
-  * {{{./apidocs/index.html}JavaDocs}}
-
-  * {{{./dependencies.html}Dependencies}}
-
diff --git a/hadoop-common-project/hadoop-common/src/site/apt/CLIMiniCluster.apt.vm b/hadoop-common-project/hadoop-common/src/site/apt/CLIMiniCluster.apt.vm
index 51a5a9afac..2d12c3905c 100644
--- a/hadoop-common-project/hadoop-common/src/site/apt/CLIMiniCluster.apt.vm
+++ b/hadoop-common-project/hadoop-common/src/site/apt/CLIMiniCluster.apt.vm
@@ -18,8 +18,6 @@
 
 Hadoop MapReduce Next Generation - CLI MiniCluster.
 
-  \[ {{{./index.html}Go Back}} \]
-
 %{toc|section=1|fromDepth=0}
 
 * {Purpose}
@@ -42,7 +40,8 @@ Hadoop MapReduce Next Generation - CLI MiniCluster.
 $ mvn clean install -DskipTests
 $ mvn package -Pdist -Dtar -DskipTests -Dmaven.javadoc.skip
 +---+
-  <<NOTE:>> You will need protoc 2.5.0 installed.
+  <<NOTE:>> You will need {{{http://code.google.com/p/protobuf/}protoc 2.5.0}}
+            installed.
 
   The tarball should be available in <<<hadoop-dist/target/>>> directory. 
 
diff --git a/hadoop-common-project/hadoop-common/src/site/apt/ClusterSetup.apt.vm b/hadoop-common-project/hadoop-common/src/site/apt/ClusterSetup.apt.vm
index 546db252b9..b4fef5d7a6 100644
--- a/hadoop-common-project/hadoop-common/src/site/apt/ClusterSetup.apt.vm
+++ b/hadoop-common-project/hadoop-common/src/site/apt/ClusterSetup.apt.vm
@@ -16,8 +16,6 @@
   ---
   ${maven.build.timestamp}
 
-  \[ {{{../index.html}Go Back}} \]
-
 %{toc|section=1|fromDepth=0}
 
 Hadoop MapReduce Next Generation - Cluster Setup
@@ -29,7 +27,7 @@ Hadoop MapReduce Next Generation - Cluster Setup
   with thousands of nodes.
 
   To play with Hadoop, you may first want to install it on a single
-  machine (see {{{SingleCluster}Single Node Setup}}).
+  machine (see {{{./SingleCluster.html}Single Node Setup}}).
 
 * {Prerequisites}
 
diff --git a/hadoop-common-project/hadoop-common/src/site/apt/CommandsManual.apt.vm b/hadoop-common-project/hadoop-common/src/site/apt/CommandsManual.apt.vm
index 857b7317fa..18114bbc3b 100644
--- a/hadoop-common-project/hadoop-common/src/site/apt/CommandsManual.apt.vm
+++ b/hadoop-common-project/hadoop-common/src/site/apt/CommandsManual.apt.vm
@@ -44,8 +44,9 @@ Overview
 Generic Options
 
    The following options are supported by {{dfsadmin}}, {{fs}}, {{fsck}},
-   {{job}} and {{fetchdt}}. Applications should implement {{{some_useful_url}Tool}} to support
-   {{{another_useful_url}GenericOptions}}.
+   {{job}} and {{fetchdt}}. Applications should implement 
+   {{{../../api/org/apache/hadoop/util/Tool.html}Tool}} to support
+   GenericOptions.
 
 *------------------------------------------------+-----------------------------+
 ||            GENERIC_OPTION                     ||            Description
@@ -123,7 +124,8 @@ User Commands
 
 * <<<fsck>>>
 
-   Runs a HDFS filesystem checking utility. See {{Fsck}} for more info.
+   Runs a HDFS filesystem checking utility.
+   See {{{../hadoop-hdfs/HdfsUserGuide.html#fsck}fsck}} for more info.
 
    Usage: <<<hadoop fsck [GENERIC_OPTIONS] <path> [-move | -delete | -openforwrite] [-files [-blocks [-locations | -racks]]]>>>
 
@@ -149,7 +151,8 @@ User Commands
 
 * <<<fetchdt>>>
 
-   Gets Delegation Token from a NameNode. See {{fetchdt}} for more info.
+   Gets Delegation Token from a NameNode.
+   See {{{../hadoop-hdfs/HdfsUserGuide.html#fetchdt}fetchdt}} for more info.
 
    Usage: <<<hadoop fetchdt [GENERIC_OPTIONS] [--webservice <namenode_http_addr>] <path> >>>
 
@@ -302,7 +305,8 @@ Administration Commands
 * <<<balancer>>>
 
    Runs a cluster balancing utility. An administrator can simply press Ctrl-C
-   to stop the rebalancing process. See Rebalancer for more details.
+   to stop the rebalancing process. See
+   {{{../hadoop-hdfs/HdfsUserGuide.html#Rebalancer}Rebalancer}} for more details.
 
    Usage: <<<hadoop balancer [-threshold <threshold>]>>>
 
@@ -445,7 +449,7 @@ Administration Commands
 * <<<namenode>>>
 
    Runs the namenode. More info about the upgrade, rollback and finalize is
-   at Upgrade Rollback
+   at {{{../hadoop-hdfs/HdfsUserGuide.html#Upgrade_and_Rollback}Upgrade Rollback}}.
 
    Usage: <<<hadoop namenode [-format] | [-upgrade] | [-rollback] | [-finalize] | [-importCheckpoint]>>>
 
@@ -474,8 +478,9 @@ Administration Commands
 
 * <<<secondarynamenode>>>
 
-   Runs the HDFS secondary namenode. See Secondary Namenode for more
-   info.
+   Runs the HDFS secondary namenode.
+   See {{{../hadoop-hdfs/HdfsUserGuide.html#Secondary_NameNode}Secondary Namenode}}
+   for more info.
 
    Usage: <<<hadoop secondarynamenode [-checkpoint [force]] | [-geteditsize]>>>
 
diff --git a/hadoop-common-project/hadoop-common/src/site/apt/Compatibility.apt.vm b/hadoop-common-project/hadoop-common/src/site/apt/Compatibility.apt.vm
index 2cd97650a2..e3c4a4daf1 100644
--- a/hadoop-common-project/hadoop-common/src/site/apt/Compatibility.apt.vm
+++ b/hadoop-common-project/hadoop-common/src/site/apt/Compatibility.apt.vm
@@ -233,9 +233,10 @@ hand-in-hand to address this.
 
     * In particular for MapReduce applications, the developer community will 
       try our best to support provide binary compatibility across major 
-      releases e.g. applications using org.apache.hadop.mapred.* APIs are 
-      supported compatibly across hadoop-1.x and hadoop-2.x. See 
-      {{{../hadoop-mapreduce-client/hadoop-mapreduce-client-core/MapReduce_Compatibility_Hadoop1_Hadoop2.html}
+      releases e.g. applications using org.apache.hadoop.mapred.
+      
+    * APIs are supported compatibly across hadoop-1.x and hadoop-2.x. See 
+      {{{../../hadoop-mapreduce-client/hadoop-mapreduce-client-core/MapReduce_Compatibility_Hadoop1_Hadoop2.html}
       Compatibility for MapReduce applications between hadoop-1.x and hadoop-2.x}} 
       for more details.
 
@@ -248,13 +249,13 @@ hand-in-hand to address this.
 
   * {{{../hadoop-hdfs/WebHDFS.html}WebHDFS}} - Stable
 
-  * {{{../hadoop-yarn/hadoop-yarn-site/ResourceManagerRest.html}ResourceManager}}
+  * {{{../../hadoop-yarn/hadoop-yarn-site/ResourceManagerRest.html}ResourceManager}}
 
-  * {{{../hadoop-yarn/hadoop-yarn-site/NodeManagerRest.html}NodeManager}}
+  * {{{../../hadoop-yarn/hadoop-yarn-site/NodeManagerRest.html}NodeManager}}
 
-  * {{{../hadoop-yarn/hadoop-yarn-site/MapredAppMasterRest.html}MR Application Master}}
+  * {{{../../hadoop-yarn/hadoop-yarn-site/MapredAppMasterRest.html}MR Application Master}}
 
-  * {{{../hadoop-yarn/hadoop-yarn-site/HistoryServerRest.html}History Server}}
+  * {{{../../hadoop-yarn/hadoop-yarn-site/HistoryServerRest.html}History Server}}
   
 *** Policy
     
@@ -512,7 +513,8 @@ hand-in-hand to address this.
     {{{https://issues.apache.org/jira/browse/HADOOP-9517}HADOOP-9517}}
 
   * Binary compatibility for MapReduce end-user applications between hadoop-1.x and hadoop-2.x -
-    {{{../hadoop-mapreduce-client/hadoop-mapreduce-client-core/MapReduce_Compatibility_Hadoop1_Hadoop2.html}MapReduce Compatibility between hadoop-1.x and hadoop-2.x}}
+    {{{../../hadoop-mapreduce-client/hadoop-mapreduce-client-core/MapReduce_Compatibility_Hadoop1_Hadoop2.html}
+    MapReduce Compatibility between hadoop-1.x and hadoop-2.x}}
 
   * Annotations for interfaces as per interface classification
     schedule -
diff --git a/hadoop-common-project/hadoop-common/src/site/apt/FileSystemShell.apt.vm b/hadoop-common-project/hadoop-common/src/site/apt/FileSystemShell.apt.vm
index 3e6fd21070..53ef0cabef 100644
--- a/hadoop-common-project/hadoop-common/src/site/apt/FileSystemShell.apt.vm
+++ b/hadoop-common-project/hadoop-common/src/site/apt/FileSystemShell.apt.vm
@@ -88,7 +88,7 @@ chgrp
 
    Change group association of files. The user must be the owner of files, or
    else a super-user. Additional information is in the
-   {{{betterurl}Permissions Guide}}.
+   {{{../hadoop-hdfs/HdfsPermissionsGuide.html}Permissions Guide}}.
 
    Options
 
@@ -101,7 +101,7 @@ chmod
    Change the permissions of files. With -R, make the change recursively
    through the directory structure. The user must be the owner of the file, or
    else a super-user. Additional information is in the
-   {{{betterurl}Permissions Guide}}.
+   {{{../hadoop-hdfs/HdfsPermissionsGuide.html}Permissions Guide}}.
 
    Options
 
@@ -112,7 +112,7 @@ chown
    Usage: <<<hdfs dfs -chown [-R] [OWNER][:[GROUP]] URI [URI ]>>>
 
    Change the owner of files. The user must be a super-user. Additional information
-   is in the {{{betterurl}Permissions Guide}}.
+   is in the {{{../hadoop-hdfs/HdfsPermissionsGuide.html}Permissions Guide}}.
 
    Options
 
@@ -210,8 +210,8 @@ expunge
 
    Usage: <<<hdfs dfs -expunge>>>
 
-   Empty the Trash. Refer to the {{{betterurl}HDFS Architecture Guide}} for
-   more information on the Trash feature.
+   Empty the Trash. Refer to the {{{../hadoop-hdfs/HdfsDesign.html}
+   HDFS Architecture Guide}} for more information on the Trash feature.
 
 get
 
@@ -439,7 +439,9 @@ test
    Options:
 
      * The -e option will check to see if the file exists, returning 0 if true.
+
      * The -z option will check to see if the file is zero length, returning 0 if true.
+
      * The -d option will check to see if the path is directory, returning 0 if true.
 
    Example:
diff --git a/hadoop-common-project/hadoop-common/src/site/apt/InterfaceClassification.apt.vm b/hadoop-common-project/hadoop-common/src/site/apt/InterfaceClassification.apt.vm
index 811cfe5410..85e66bd9a6 100644
--- a/hadoop-common-project/hadoop-common/src/site/apt/InterfaceClassification.apt.vm
+++ b/hadoop-common-project/hadoop-common/src/site/apt/InterfaceClassification.apt.vm
@@ -18,8 +18,6 @@
 
 Hadoop Interface Taxonomy: Audience and Stability Classification
 
-  \[ {{{./index.html}Go Back}} \]
-
 %{toc|section=1|fromDepth=0}
 
 * Motivation
diff --git a/hadoop-common-project/hadoop-common/src/site/apt/ServiceLevelAuth.apt.vm b/hadoop-common-project/hadoop-common/src/site/apt/ServiceLevelAuth.apt.vm
index 467598d4fd..258819e110 100644
--- a/hadoop-common-project/hadoop-common/src/site/apt/ServiceLevelAuth.apt.vm
+++ b/hadoop-common-project/hadoop-common/src/site/apt/ServiceLevelAuth.apt.vm
@@ -29,8 +29,10 @@ Service Level Authorization Guide
 
    Make sure Hadoop is installed, configured and setup correctly. For more
    information see:
-     * Single Node Setup for first-time users.
-     * Cluster Setup for large, distributed clusters.
+
+     * {{{./SingleCluster.html}Single Node Setup}} for first-time users.
+
+     * {{{./ClusterSetup.html}Cluster Setup}} for large, distributed clusters.
 
 * Overview
 
diff --git a/hadoop-common-project/hadoop-common/src/site/apt/SingleCluster.apt.vm b/hadoop-common-project/hadoop-common/src/site/apt/SingleCluster.apt.vm
index c86cd6defd..cf8390e461 100644
--- a/hadoop-common-project/hadoop-common/src/site/apt/SingleCluster.apt.vm
+++ b/hadoop-common-project/hadoop-common/src/site/apt/SingleCluster.apt.vm
@@ -18,8 +18,6 @@
 
 Hadoop MapReduce Next Generation - Setting up a Single Node Cluster.
 
-  \[ {{{./index.html}Go Back}} \]
-
 %{toc|section=1|fromDepth=0}
 
 * Mapreduce Tarball
@@ -32,7 +30,8 @@ $ mvn clean install -DskipTests
 $ cd hadoop-mapreduce-project
 $ mvn clean install assembly:assembly -Pnative
 +---+
-  <<NOTE:>> You will need protoc 2.5.0 installed.
+  <<NOTE:>> You will need {{{http://code.google.com/p/protobuf}protoc 2.5.0}}
+            installed.
 
   To ignore the native builds in mapreduce you can omit the <<<-Pnative>>> argument
   for maven. The tarball should be available in <<<target/>>> directory. 
diff --git a/hadoop-hdfs-project/hadoop-hdfs/CHANGES.txt b/hadoop-hdfs-project/hadoop-hdfs/CHANGES.txt
index c430f451af..198566bcf9 100644
--- a/hadoop-hdfs-project/hadoop-hdfs/CHANGES.txt
+++ b/hadoop-hdfs-project/hadoop-hdfs/CHANGES.txt
@@ -1151,6 +1151,9 @@ Release 2.3.0 - UNRELEASED
     HDFS-5343. When cat command is issued on snapshot files getting unexpected result.
     (Sathish via umamahesh)
 
+    HADOOP-9982. Fix dead links in hadoop site docs. (Akira Ajisaka via Arpit
+    Agarwal)
+
 Release 2.2.0 - 2013-10-13
 
   INCOMPATIBLE CHANGES