fix doxygen setup and automate generation

rakefile for some common tasks and doxygen needs
to look in the new place for headers

Rakefile

+desc "Build and Run Tests"
+task :build do
+  `./waf clean`
+  `./waf clean-tests`
+  `./waf configure`
+  `./waf build`
+  `./waf test`
+end
+
+desc "Build docs"
+task :docs do
+  puts "Generating Doxygen docs"
+  `doxygen api.doxygen`
+  `git stash`
+  `git checkout gh-pages`
+  `cp -Rf apidocs/html/* .`
+  `git add .`
+  `git commit -am 'generated docs'`
+  `git push origin gh-pages`
+  `git checkout master`
+end

api.doxygen

 PROJECT_NAME = libgit2
 
-INPUT            = src/git
+INPUT            = src/git2
 QUIET            = YES
 RECURSIVE        = YES
 FILE_PATTERNS    = *.h