If Rails version is in Gemfile, use it

and process Gemfile before config, because config location
depends on Rails version.

Fixes #398

lib/brakeman/processors/gem_processor.rb

@@ -19,6 +19,11 @@ class Brakeman::GemProcessor < Brakeman::BaseProcessor
       @tracker.config[:rails_version] = $1
     end
 
+    if @tracker.config[:rails_version] =~ /^(3|4)\./ and not @tracker.options[:rails3]
+      @tracker.options[:rails3] = true
+      Brakeman.notify "[Notice] Detected Rails #$1 application"
+    end
+
     if @tracker.config[:gems][:rails_xss]
       @tracker.config[:escape_html] = true
 

lib/brakeman/scanner.rb

@@ -47,10 +47,10 @@ class Brakeman::Scanner
 
   #Process everything in the Rails application
   def process
-    Brakeman.notify "Processing configuration..."
-    process_config
     Brakeman.notify "Processing gems..."
     process_gems
+    Brakeman.notify "Processing configuration..."
+    process_config
     Brakeman.notify "Processing initializers..."
     process_initializers
     Brakeman.notify "Processing libs..."