Proper PR with the changes requested

wiki/BioJava_BioSQL_ORM.md

@@ -11,7 +11,7 @@ to objects in the `org.biojavax` packages.
 BioJavaX Design
 ===============
 
-[BioJavaX](http://biojava.org/wikis/BioJava:BioJavaXDocs/) was officially
+[BioJavaX](http://biojava.org/wiki/BioJava%3ABioJavaXDocs) was officially
 released with BioJava1.5. It extends the `org.biojava` API's and was
 designed to very closely match the BioSQL schema. This made ORM of
 [BioJava](http://biojava.org) to BioSQL much more straight forward
@@ -27,10 +27,10 @@ files formally define where objects are written in the database.
 
 Hibernate mappings are currently defined for the following RDBMS's:
 
--   [PostGres](http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/trunk/src/org/biojavax/bio/db/biosql/pg)
--   [Oracle](http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/trunk/src/org/biojavax/bio/db/biosql/oracle)
--   [MySQL](http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/trunk/src/org/biojavax/bio/db/biosql/mysql)
--   [HyperSonic](http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/trunk/src/org/biojavax/bio/db/biosql/hsqldb)
+-   [PostGres](https://github.com/biojava/biojava-legacy/tree/master/biosql/src/main/java/org/biojavax/bio/db/biosql/pg)
+-   [Oracle](https://github.com/biojava/biojava-legacy/tree/master/biosql/src/main/java/org/biojavax/bio/db/biosql/oracle)
+-   [MySQL](https://github.com/biojava/biojava-legacy/tree/master/biosql/src/main/java/org/biojavax/bio/db/biosql/mysql)
+-   [HyperSonic](https://github.com/biojava/biojava-legacy/tree/master/biosql/src/main/java/org/biojavax/bio/db/biosql/hsqldb)
 -   Derby (comming soon)
 
 JPA and Annotations

wiki/Enhancement_Requests.md

@@ -237,7 +237,7 @@ that seems like a bastardization. Suggestions welcome.
 ### Ability to fully represent contig assembly
 
 The ability to fully represent [EMBL format's CO
-lines](http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_4_14)
+lines](http://ftp.ebi.ac.uk/pub/databases/embl/doc/usrman.txt#3_4_14)
 in a BioSQL record would be desirable. The CO line is essentially a join
 of segments of other sequences, like this:
 
@@ -282,7 +282,7 @@ would only consist of gap characters, and be virtual).
 Should there be a better way of doing this?
 
 Related to CO lines, [EMBLs AS
-lines](http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html#3_4_13)
+lines](http://ftp.ebi.ac.uk/pub/databases/embl/doc/usrman.txt#3_4_13)
 store assembly path information. In essence, these could be stored as
 feature pairs, one feature on the source contig (or read, another
 bioentry), the other feature on the assembled contig (the entry with the

wiki/Main_Page.md

@@ -113,10 +113,10 @@ Contacts
 Project lead is [Hilmar Lapp](http://lappland.io). Questions
 should be sent to the BioSQL mailing list at
 [biosql-l@lists.open-bio.org](mailto:biosql-l%40lists%2eopen-bio%2eorg).
-You can also [subscribe](http://open-bio.org/mailman/listinfo/biosql-l)
+You can also [subscribe](http://mailman.open-bio.org/mailman/listinfo/biosql-l)
 to the mailing list to keep up to date with discussions and
 announcements.
 
 In addition, the [biosql-guts
-list](http://open-bio.org/mailman/listinfo/biosql-guts-l) is for bug
+list](http://mailman.open-bio.org/mailman/listinfo/biosql-guts-l) is for bug
 tracking and commit messages.

wiki/PhyloDBSchema.md

@@ -82,7 +82,7 @@ part of. "left\_idx and "right\_idx" specify the left and right values
 of the nested set optimization structure for efficient hierarchical
 queries. These values needs to be precomputed by a program, see [J.
 Celko, SQL for
-Smarties](http://rs18.rapidshare.com/files/4441805/Trees_and_Hierarchies_in_SQL_for_Smarties.pdf).
+Smarties](https://www.worldcat.org/search?q=isbn%3A0128007613).
 
 NODE\_PATH
 ----------

wiki/Releases.md

@@ -90,11 +90,11 @@ on any of the below, please email them to biosql-l@lists.open-bio.org.
 5.  Update Changes file. *Done. --[Hilmar](http://lappland.io)
     23:41, 22 February 2008 (EST)*
 6.  Update documentation in the repository. *Done, for
-    [Biopython](http://code.open-bio.org/svnweb/index.cgi/biosql/browse/biosql-schema/trunk/doc/biopython)
+    [Biopython](https://github.com/biosql/biosql/tree/master/doc/biopython)
     (see
-    [PDF](http://code.open-bio.org/svnweb/index.cgi/biosql/checkout/biosql-schema/trunk/doc/biopython/python_biosql_basic.pdf))
+    [PDF](https://github.com/biosql/biosql/blob/master/doc/biopython/python_biosql_basic.pdf))
     and
-    [BioJava/Oracle](http://code.open-bio.org/svnweb/index.cgi/biosql/checkout/biosql-schema/trunk/doc/bj_and_bsql_oracle_howto.htm).
+    [BioJava/Oracle](https://github.com/biosql/biosql/blob/master/doc/bj_and_bsql_oracle_howto.htm).
     Unfortunately, realized this not before, but only after branching
     off, so need to merge all changes to the branch.
     --[Hilmar](http://lappland.io) 12:06, 24 February 2008 (EST)*