org Formatting in the doc

README.org

+The Pipelet Readme
+
 Pipelet is a free framework allowing for the creation, execution and
 browsing of scientific data processing pipelines. It provides:
 
@@ -56,7 +58,7 @@ You may find useful to install some generic scientific tools that nicely interac
 
 There is not any published stable release of Pipelet right now.
 
-git clone git://gitorious.org/pipelet/pipelet.git
+=git clone git://gitorious.org/pipelet/pipelet.git=
 
 **** Installing Pipelet
 
@@ -66,17 +68,19 @@ sudo python setup.py install
 
 1. Run the test pipeline
 
-cd test/first_test
-python main.py
+=cd test/first_test=
+
+=python main.py=
 
 2. Add this pipeline to the web interface
 
-pipeweb track test ./.sqlstatus
+=pipeweb track test ./.sqlstatus=
 
 3. Set the access control and launch the web server
 
-pipeutils -a username -l 2 .sqlstatus
-pipeweb start
+=pipeutils -a username -l 2 .sqlstatus=
+
+=pipeweb start=
 
 4. You should be able to browse the result on the web page
    http://localhost:8080
@@ -85,7 +89,7 @@ pipeweb start
 
 To get a new pipeline framework, with example main and segment scripts : 
 
-pipeutils -c pipename
+=pipeutils -c pipename=
 
 This command ends up with the creation of directory named pipename wich contains: 
 + a main script (named main.py) providing functionnalities to execute
@@ -109,12 +113,16 @@ The dependencies between segments must form a directed acyclic
 graph. This graph is described by a char string using a subset of the
 graphviz dot language (http://www.graphviz.org). For example the string:
 
+
 """
-a -> b -> d;
-c -> d;
-c -> e;
+=a -> b -> d;=
+
+=c -> d;=
+
+=c -> e;=
 """
 
+
 defines a pipeline with 5 segments {"a", "b", "c", "d", "e"}. The
 relation "a->b" ensures that the processing of the segment "a" will be
 done before the processing of its child segment "b". Also the output
@@ -129,8 +137,8 @@ named "se.py" and "s.py". This way, different segments of the pipeline
 can share the same code, if they are given a name with a common root
 (this mechanism is useful to write generic segment and is completed by
 the hooking system, described in the advanced usage section). The code
-is then executed in a specific namespace (see below The execution
-environment).
+is then executed in a specific namespace (see below [[*The%20segment%20environment][The execution
+environment]]).
 
 *** The Pipeline object
 
@@ -140,7 +148,7 @@ P = Pipeline(pipedot, codedir=, prefix=)
 
 - pipedot is the string description of the pipeline
 - codedir is the path where the segment scripts can be found
-- prefix  is the path to the data repository (see below Hierarchical data storage)
+- prefix  is the path to the data repository (see below [[*Hierarchical%20data%20storage][Hierarchical data storage]])
 
 It is possible to output the graphviz representation of the pipeline
 (needs graphviz installed). First, save the graph string into a .dot
@@ -206,8 +214,8 @@ final output set of segment "melt" will be:
  [('Lancelot the Brave'), ('Lancelot the Pure'), ('Galahad the Brave'), ('Galahad the Pure')].
 
 This default behavior can be altered by specifying a #multiplex
-directive in the commentary of the segment code. See section Multiplex
-directive for more details.
+directive in the commentary of the segment code. See section [[*Multiplex%20directive][Multiplex
+directive]] for more details.
 
 As the segment execution order is not uniquely determined by the pipe
 scheme (several path may exists), it is not possible to retrieve an
@@ -218,7 +226,7 @@ above example, one can read "melt" inputs using:
 k = seg_input["knights"]
 q = seg_input["quality"]
 
-See section 'The segment environment' for more details. 
+See section [[*The%20segment%20environment]['The segment environment']] for more details.
 
 *** Orphan segments
 
@@ -236,7 +244,7 @@ id = seg_input['segnamephantom']
 or
 id = seg_input.values()[0]
 
-See section 'The segment environment' for more details. 
+See section [[*The%20segment%20environment][The segment environment]] for more details.
 
 *** Hierarchical data storage
 
@@ -311,7 +319,7 @@ The segment code is executed in a specific environment that provides:
    Pipelet enables you to write reusable generic
    segments by providing a hooking system via the hook function.
    hook (hookname, globals()): execute Python script ‘segname_hookname.py’ and update the namespace.
-   See the Hooking system for more details.
+   See the section [[*the%20Hooking%20system][Hooking system]] for more details.
 
 
 *** The example pipelines
@@ -680,6 +688,7 @@ Logs are ordered by date.
 * Advanced usage
 
 ** Multiplex directive
+   
 
 The default behavior can be altered by specifying a #multiplex
 directive in the commentary of the segment code. If several multiplex
@@ -729,7 +738,7 @@ Another caution on the use of group: segment input data type is no
 longer a dictionary in those cases as the original tuple is
 transformed but simply the result of the class function.
 
-See section 'The segment environment' for more details.
+See section [[*The%20segment%20environment][The segment environment]] for more details.
 
 ** Depend directive
 
@@ -816,8 +825,8 @@ File : myenvironment.py
 
 
 The Pipelet engine objects (segments, tasks, pipeline) are available
-from the worker attribut self._worker. See section "The Pipelet
-actors" for more details about the Pipelet machinery.
+from the worker attribut self._worker. See section [[*the%20pipelet%20actors][The Pipelet actors]]
+for more details about the Pipelet machinery.
 
 
 *** Writing new environment
@@ -850,8 +859,8 @@ The segment output argument has to be returned by the _close(self, glo)
 method. 
 
 The pipelet engine objects (segments, tasks, pipeline) are available
-from the worker attribut self._worker. See section "The Pipelet
-actors" for more details about the Pipelet machinery.
+from the worker attribut self._worker. See section [[*the%20pipelet%20actors][The Pipelet
+actors]] for more details about the Pipelet machinery.
 
 
 *** Loading another environment
@@ -869,11 +878,11 @@ Pipeweb use the cherrypy web framework server and can be run behind an
 apache webserver which brings essentially two advantages:
 - https support.
 - faster static files serving.
-See the cherrypy documentation for hints about this.
+See the [[http://www.cherrypy.org/wiki/TableOfContents][cherrypy]] documentation for hints about this.
 
-* The pipelet actors
+* The Pipelet actors
   
-This section document the code for developpers.
+This section document the code for developers.
 The code documentation can be built using the doxygen configuration
 file