Removed defunct project files, added README and renamed COPYING to LI…

…CENSE to be more GitHub-friendly.

.project

@@ -5,7 +5,13 @@
 	<projects>
 	</projects>
 	<buildSpec>
+		<buildCommand>
+			<name>com.aptana.ide.core.unifiedBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
 	</buildSpec>
 	<natures>
+		<nature>com.aptana.projects.webnature</nature>
 	</natures>
 </projectDescription>

NEWS

@@ -4,7 +4,7 @@ Bowtie 2 NEWS
 Bowtie 2 is now available for download from the project website,
 http://bowtie-bio.sf.net/bowtie2.  2.0.0-beta1 is the first version released to
 the public and 2.0.5 is the latest version.  Bowtie 2 is licensed under
-the GPLv3 license.  See `COPYING' file for details.
+the GPLv3 license.  See `LICENSE' file for details.
 
 Reporting Issues
 ================
@@ -25,6 +25,7 @@ Version 2.0.5 - December 19, 2012
      that invalid index files don't linger.
    * Tokenizer no longer has limit of 10,000 tokens, which was a problem for
      users trying to index a very large number of FASTA files.
+   * Renamed COPYING to LICENSE and created a README to be GitHub-friendly.
 
 Version 2.0.4 - December 17, 2012
    * Fixed issue whereby --un, --al, --un-conc and --al-conc options would

README

@@ -0,0 +1,8 @@
+Bowtie 2: http://bowtie-bio.sf.net/bowtie2
+
+ - See AUTHORS for information about who wrote Bowtie 2 and its various
+   components.
+ - See LICENSE for license information.
+ - See MANUAL for detailed information on how to use Bowtie 2.
+ - See NEWS for information about changes in this and previous versions
+   of Bowtie 2.