fixing all wiki links to point to correct URL when rendered in Jekyll

Author: andreasprlic

_wikis/BioJava3:Coding_Conventions.md

@@ -3,11 +3,11 @@ title: BioJava3:Coding Conventions
 ---
 
 -   Each file should contain the
-    [BioJava3\_license](BioJava3_license "wikilink") LGPL copyright
+    [BioJava3\_license](/wikis/BioJava3_license "wikilink") LGPL copyright
     statement.
 
 <!-- -->
 
 -   For Eclipse developers, here a Code template:
-    [BioJava3\_eclipse\_template](BioJava3_eclipse_template "wikilink")
+    [BioJava3\_eclipse\_template](/wikis/BioJava3_eclipse_template "wikilink")
 

_wikis/BioJava3_Design.md

@@ -12,7 +12,7 @@ Implementation
 --------------
 
 For information on the current status of the BioJava 3 implementation go
-to [BioJava3\_project](BioJava3_project "wikilink")
+to [BioJava3\_project](/wikis/BioJava3_project "wikilink")
 
 References
 ----------
@@ -214,4 +214,4 @@ Use cases
 
 It is planned to document BioJava in parallel with development. To do
 this, we want to drive development from a set of [ use
-cases](BioJava 3 Use Cases "wikilink").
+cases](/wikis/BioJava 3 Use Cases "wikilink").

_wikis/BioJava3_Feature_Requests.md

@@ -21,5 +21,5 @@ There are also a number of algorithms where we would be interested in
 [Java ports](Algorithm_Java_port "wikilink").
 
 You can also take a look at the current list of [ BioJava
-Modules](BioJava:Modules#BioJava_3.0.X "wikilink") and suggest other
+Modules](/wikis/BioJava:Modules#BioJava_3.0.X "wikilink") and suggest other
 missing features.

_wikis/BioJava3_Proposal.md

@@ -8,7 +8,7 @@ BioJava 3 has been released
 This page was used while starting the discussions for creating the new
 version. BioJava 3.0 has been released on Dec. 28th 2010.
 
-[BioJava3\_project](BioJava3_project "wikilink")
+[BioJava3\_project](/wikis/BioJava3_project "wikilink")
 
 Executive Summary
 -----------------

_wikis/BioJava3_eclipse.md

@@ -113,7 +113,7 @@ require SCM handler.*
     files (the maven config files) and will understand that it is a
     maven and a git-tracked project.
 
-You should now have source to all the biojava modules (biojava3-core,
+You should now have source to all the biojava modules (/wikis/BioJava3-core,
 biojava3-structure, etc). Viewing the history for any file should show
 you all commits since 2009 which have contributed to that file.
 

_wikis/BioJava3_license.md

@@ -3,7 +3,7 @@ title: BioJava3 license
 ---
 
 BioJava 3 is using the [standard BioJava
-license](BioJava:License "wikilink"): LGPL v 2.1
+license](/wikis/BioJava:License "wikilink"): LGPL v 2.1
 
 Developers: Please include the following javadoc in the header of every
 class you commit:

_wikis/BioJava3_project.md

@@ -23,7 +23,7 @@ how to check out the code from SVN or get the latest SNAPSHOT builds.
 IDE specific instructions
 -------------------------
 
--   [BioJava3\_eclipse](BioJava3_eclipse "wikilink") how to work with
+-   [BioJava3\_eclipse](/wikis/BioJava3_eclipse "wikilink") how to work with
     BioJava3 using eclipse
 
 Wanted
@@ -42,13 +42,13 @@ Coding conventions
 ------------------
 
 -   We are using Maven to build biojava 3
--   [BioJava3\_license](BioJava3_license "wikilink") - All source code
+-   [BioJava3\_license](/wikis/BioJava3_license "wikilink") - All source code
     of BioJava 3 is under LGPL.
--   [BioJava3\_logging](BioJava3_logging "wikilink") - How to use
+-   [BioJava3\_logging](/wikis/BioJava3_logging "wikilink") - How to use
     logging
 
 Links
 -----
 
--   [BioJava3\_Proposal](BioJava3_Proposal "wikilink")
+-   [BioJava3\_Proposal](/wikis/BioJava3_Proposal "wikilink")
 

_wikis/BioJava:1.5ReleasePlan.md

@@ -106,10 +106,10 @@ consideration.
 
 ### Documentation
 
--   Update [Cookbook](BioJava:Cookbook "wikilink") code to reflect best
+-   Update [Cookbook](/wikis/BioJava:Cookbook "wikilink") code to reflect best
     practices with BioJavaX
 -   Should we keep legacy examples in the
-    [Cookbook](BioJava:Cookbook "wikilink")?
+    [Cookbook](/wikis/BioJava:Cookbook "wikilink")?
 -   Check for errors in biojavax docbook
 
 ### Javadoc