Created a simple Java interface to run-span called clj-span.core/java-span-bridge.

- Updated .gitignore to handle all lein2 outputs.
- Updated project.clj to lein2 and clojure 1.4.0.
Began to create the template for a line-of-sight model literate program.
Fixing a minor typo (standard deviation -> variance) in resources/java-span-bridge-api.java.
Fixing some minor bugs with the new java-span-bridge API.
Removing some old writing files (moved them to my Thesis directory where they belong).
Upgraded to newest Clojure 1.5.0-RC16.
Added the only interesting code from Tucci's clj-span.gui project as clj-span.gui-simple.
Added efficiency-related comments to clj-span.models.line-of-sight (no source code changes though).
Pulled java-span-bridge code out of clj-span.core into clj-span.java-span-bridge.
Updated clj-span.java-span-bridge to accept input map layers organized as 1D double arrays rather than 2D double arrays.
Updated clj-span.java-span-bridge/run-span to take and return layers represented as 1D Java arrays.
Minor tweak to project.clj to make clj-span.java-span-bridge AOT compile and stupid fix to its API docs.
Patched clj-span.java-span-bridge to expose runSpan as a public static method via its Java API.
Patching a fatal bug that occurs whenever downscaling-factor is a floating point number.
Upgraded to Clojure 1.5.0. Yeah! (also tweaked the formatting for a log message)
Updating the dates in all source file copyright headers.
Upgraded to Clojure 1.5.1 and added dependencies on clj-jts and integratedmodelling/thinklab-api.
Updating copyright headers in the models/ directory.
Moved the (shutdown-agents)(flush) code from clj-span.commandline to clj-span.core.
Major overhaul of the line-of-sight model! Go Ioannis Go!