Doc update to please Doxygen

Doxygen doesn't like when a =head2 section is not linked to a method.
We had to move the comments to #-prefixed lines.

modules/Bio/EnsEMBL/Hive/Process.pm

@@ -224,12 +224,9 @@ sub param_defaults {
 }
 
 
-=head2 pre_cleanup
-
-    Title   :  pre_cleanup
-    Function:  sublcass can implement functions related to cleaning up the database/filesystem after the previous unsuccessful run.
-               
-=cut
+#
+## Function: sublcass can implement functions related to cleaning up the database/filesystem after the previous unsuccessful run.
+#
 
 # sub pre_cleanup {
 #    my $self = shift;
@@ -289,13 +286,10 @@ sub write_output {
 }
 
 
-=head2 post_cleanup
-
-    Title   :  post_cleanup
-    Function:  sublcass can implement functions related to cleaning up after running one job
-               (destroying non-trivial data structures in memory).
-               
-=cut
+#
+## Function:  sublcass can implement functions related to cleaning up after running one job
+#               (destroying non-trivial data structures in memory).
+#
 
 #sub post_cleanup {
 #    my $self = shift;

modules/Bio/EnsEMBL/Hive/RunnableDB/JobFactory.pm

@@ -26,6 +26,11 @@
 
         param('inputcmd');   The list is generated by running a system command: 'inputcmd' => 'find /tmp/big_directory -type f'
 
+    NB for developpers: fetch_input() method is intentionally missing from JobFactory.pm .
+    If JobFactory is subclassed (say, by a Compara RunnableDB) the child class's should use fetch_input()
+    to set $self->param('inputlist') to whatever list of ids specific to that particular type of data (slices, members, etc).
+    The rest functionality will be taken care for by the parent class code.
+
 =head1 LICENSE
 
     Copyright [1999-2014] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
@@ -72,20 +77,6 @@ sub param_defaults {
 }
 
 
-=head2 fetch_input
-
-    Description : Implements fetch_input() interface method of Bio::EnsEMBL::Hive::Process that is used to read in parameters and load data.
-                  Here we have nothing to do.
-                  
-                  NB: This method is intentionally missing from JobFactory.pm .
-
-                  If JobFactory is subclassed (say, by a Compara RunnableDB) the child class's should use fetch_input()
-                  to set $self->param('inputlist') to whatever list of ids specific to that particular type of data (slices, members, etc).
-                  The rest functionality will be taken care for by the parent class code.
-
-=cut
-
-
 
 =head2 run