diff --git a/documentation/winelib-bindlls.sgml b/documentation/winelib-bindlls.sgml
index f8a61b36f48..7afb5760473 100644
--- a/documentation/winelib-bindlls.sgml
+++ b/documentation/winelib-bindlls.sgml
@@ -224,7 +224,7 @@ signed short WINAPI MyProxyWinFunc (unsigned short a, void *b, void *c,
         </itemizedlist>
       </para>
       <para>
-        After running winemaker I like to edit the Makefile.in to add the line
+        After running winemaker I like to edit the Makefile to add the line
         CEXTRA = -Wall just before the DEFINES =.
       </para>
       <para>
diff --git a/documentation/winelib-intro.sgml b/documentation/winelib-intro.sgml
index e0e41319159..a00bc3f61ed 100644
--- a/documentation/winelib-intro.sgml
+++ b/documentation/winelib-intro.sgml
@@ -399,23 +399,6 @@
               </para>
             </listitem>
           </varlistentry>
-          <varlistentry>
-            <term><option>Running the configure script</option></term>
-            <listitem>
-              <para>
-                Before you run <command>make</command> you must run the
-                autoconf <command>configure</command> script. The goal of this
-                step is to analyze your system and generate customized
-                makefiles from the <filename>Makefile.in</filename> files. This
-                is also when you have to tell where Winelib resides on your
-                system. If wine is installed in a single directory or you have
-                the Wine sources compiled somewhere then you can just run
-                <command>./configure --with-wine=/usr/local/bin</command>
-                or <command>./configure --with-wine=~/wine</command>
-                respectively.
-              </para>
-            </listitem>
-          </varlistentry>
           <varlistentry>
             <term><option>Running make</option></term>
             <listitem>
@@ -427,9 +410,10 @@
                 <itemizedlist>
                   <listitem>
                     <para>
-                      review the <filename>Makefile.in</filename> files to
-                      adjust the default compilation and link options set by
-                      winemaker. See the <xref linkend="source-analysis"
+                      review the <filename>Makefile</filename> files to
+                      adjust what winemaker thinks are the binaries you are
+                      trying to build and which sources should be used for
+                      each. See the <xref linkend="source-analysis"
                       endterm="source-analysis.title"> section for some hints.
                     </para>
                   </listitem>
@@ -442,12 +426,6 @@
                   </listitem>
                 </itemizedlist>
               </para>
-              <para>
-                If you find yourself modifying the Makefile.in to specify the
-                location of the Wine header or library files then go back to
-                the previous step (the configure script) and use the various
-                --with-wine-* options to specify where they are.
-              </para>
             </listitem>
           </varlistentry>
         </variablelist>
diff --git a/documentation/winelib-toolkit.sgml b/documentation/winelib-toolkit.sgml
index 6ce2a55f2ca..a13d21da69f 100644
--- a/documentation/winelib-toolkit.sgml
+++ b/documentation/winelib-toolkit.sgml
@@ -61,7 +61,7 @@
         <para>
           First are executables and DLLs. Each time it finds one of these in 
           a directory, winemaker puts it in the list of things to build and 
-          will later generate a <filename>Makefile.in</filename> file in this 
+          will later generate a <filename>Makefile</filename> file in this 
           directory. Note that Winemaker also knows about the commonly used 
           <filename>Release</filename> and <filename>Debug</filename> 
           directories, so it will attribute the executables and libraries 
@@ -109,7 +109,7 @@
           these targets based on their names. Source files that do not seem 
           to match any specific target are put in a global list for this 
           directory, see the <literal>EXTRA_xxx</literal> variables in the 
-          <filename>Makefile.in</filename>, and linked with each of the 
+          <filename>Makefile</filename>, and linked with each of the 
           targets. The assumption here is that these source files contain 
           common code which is shared by all the targets.
           If no targets were found in the directory where these files are 
@@ -151,10 +151,8 @@
           <option>--nolower-include</option>).
         </para>
         <para>
-          Finally winemaker generates the <filename>Makefile.in</filename> 
-          files and other support files (wrapper files, spec files, 
-          <filename>configure.in</filename>, 
-          <filename>Make.rules.in</filename>). From the above description 
+          Finally winemaker generates the <filename>Makefile</filename> 
+          files. From the above description 
           you can guess at the items that winemaker may get wrong in 
           this phase: macro definitions, include path, DLL path, DLLs to
           import, library path, libraries to link with. You can deal with
@@ -173,7 +171,7 @@
           others will not compile if it is. Fortunately all the files in a 
           given source tree use the same setting so that all you have to do 
           is add <literal>-DSTRICT</literal> on winemaker's command line 
-          or in the <filename>Makefile.in</filename> file(s).
+          or in the <filename>Makefile</filename> file(s).
         </para>
         <para>
           Finally the most likely reasons for missing or duplicate symbols 
@@ -186,7 +184,7 @@
               being linked with the right set of libraries. You can avoid
               this by using winemaker's <option>-P</>, <option>-i</>,
               <option>-L</option> and <option>-l</> options or adding these
-              DLLs and libraries to the <filename>Makefile.in</> file.
+              DLLs and libraries to the <filename>Makefile</> file.
             </para>
           </listitem>
           <listitem>
@@ -194,7 +192,7 @@
               Maybe you have multiple targets in a single directory and 
               winemaker guessed wrong when trying to match the source files 
               with the targets. The only way to fix this kind of problem is 
-              to edit the <filename>Makefile.in</filename> file manually.
+              to edit the <filename>Makefile</filename> file manually.
             </para>
           </listitem>
           <listitem>
@@ -204,7 +202,7 @@
               sibling directory, e.g. if you link with 
               <filename>../hello/world.o</filename> then you will get missing 
               symbols. Again the only solution is to manually edit the 
-              <filename>Makefile.in</filename> file.
+              <filename>Makefile</filename> file.
             </para>
           </listitem>
         </itemizedlist>
@@ -219,18 +217,10 @@
         </para>
       </sect2>
 
-      <sect2 id="Makefile.in">
-        <title id="Makefile.in.title">The Makefile.in files</title>
-        <para>
-          The <filename>Makefile.in</filename> is your makefile. More 
-          precisely it is the template from which the actual makefile will 
-          be generated by the <filename>configure</filename> script. It also 
-          relies on the <filename>Make.rules</filename> file for most of 
-          the actual logic. This way it only contains a relatively simple 
-          description of what needs to be built, not the complex logic of 
-          how things are actually built.
-        </para>
+      <sect2 id="Makefile">
+        <title id="Makefile.title">The Makefile files</title>
         <para>
+          The <filename>Makefile</filename> is your makefile.
           So this is the file to modify if you want to customize things. 
           Here's a detailed description of its content:
         </para>
@@ -247,7 +237,7 @@ VPATH                 = @srcdir@
           variables make it possible to have per-architecture directories for 
           compiled files and other similar goodies (But note that this kind 
           of functionality has not been tested with winemaker generated 
-          <filename>Makefile.in</filename> files yet).
+          <filename>Makefile</filename> files yet).
         </para>
         <programlisting>
 SUBDIRS               =
@@ -407,20 +397,6 @@ ENDS)
           to modify them.
         </para>
       </sect2>
-
-      <sect2 id="Make.rules.in">
-        <title id="Make.rules.in.title">The Make.rules.in file</title>
-        <para>
-          What's in the Make.rules.in...
-        </para>
-      </sect2>
-
-      <sect2 id="configure.in">
-        <title id="configure.in.title">The configure.in file</title>
-        <para>
-          What's in the configure.in...
-        </para>
-      </sect2>
     </sect1>
 
     <sect1 id="wrc">