diff --git a/lib/brakeman.rb b/lib/brakeman.rb
index 2a8723c811e1ff3d07b9e0294b642d868437b6db..84a49aa995ed6d1596e07c7fe0bb864eb075cb70 100644
--- a/lib/brakeman.rb
+++ b/lib/brakeman.rb
@@ -8,6 +8,9 @@ module Brakeman
   #option is set
   Warnings_Found_Exit_Code = 3
 
+  @debug = false
+  @quiet = false
+
   #Run Brakeman scan. Returns Tracker object.
   #
   #Options:
@@ -42,10 +45,10 @@ module Brakeman
   def self.run options
     options = set_options options
 
-    if options[:quiet]
-      options[:report_progress] = false
-      $VERBOSE = nil
-    end
+    @quiet = !!options[:quiet]
+    @debug = !!options[:debug]
+
+    options[:report_progress] = !@quiet
 
     scan options
   end
@@ -68,7 +71,7 @@ module Brakeman
 
     if File.exist? app_path + "/script/rails"
       options[:rails3] = true
-      warn "[Notice] Detected Rails 3 application" 
+      notify "[Notice] Detected Rails 3 application"
     end
 
     options
@@ -86,7 +89,7 @@ module Brakeman
       "#{File.expand_path(File.dirname(__FILE__))}/../lib/config.yaml"].each do |f|
 
       if File.exist? f and not File.directory? f
-        warn "[Notice] Using configuration in #{f}" unless options[:quiet]
+        notify "[Notice] Using configuration in #{f}"
         options = YAML.load_file f
         options.each do |k,v|
           if v.is_a? Array
@@ -173,7 +176,7 @@ module Brakeman
     require 'fileutils'
 
     if not File.exists? "lib/tasks"
-      warn "Creating lib/tasks"
+      notify "Creating lib/tasks"
       FileUtils.mkdir_p "lib/tasks"
     end
 
@@ -182,10 +185,10 @@ module Brakeman
     FileUtils.cp "#{path}/brakeman/brakeman.rake", "lib/tasks/brakeman.rake"
 
     if File.exists? "lib/tasks/brakeman.rake"
-      warn "Task created in lib/tasks/brakeman.rake"
-      warn "Usage: rake brakeman:run[output_file]"
+      notify "Task created in lib/tasks/brakeman.rake"
+      notify "Usage: rake brakeman:run[output_file]"
     else
-      warn "Could not create task"
+      notify "Could not create task"
     end
   end
 
@@ -219,7 +222,7 @@ module Brakeman
   #Run a scan. Generally called from Brakeman.run instead of directly.
   def self.scan options
     #Load scanner
-    warn "Loading scanner..."
+    notify "Loading scanner..."
 
     begin
       require 'brakeman/scanner'
@@ -230,27 +233,27 @@ module Brakeman
     #Start scanning
     scanner = Scanner.new options
 
-    warn "[Notice] Using Ruby #{RUBY_VERSION}. Please make sure this matches the one used to run your Rails application."
+    notify "[Notice] Using Ruby #{RUBY_VERSION}. Please make sure this matches the one used to run your Rails application."
 
-    warn "Processing application in #{options[:app_path]}"
+    notify "Processing application in #{options[:app_path]}"
     tracker = scanner.process
 
     if options[:parallel_checks]
-      warn "Running checks in parallel..."
+      notify "Running checks in parallel..."
     else
-      warn "Runnning checks..."
+      notify "Runnning checks..."
     end
     tracker.run_checks
 
     if options[:output_file]
-      warn "Generating report..."
+      notify "Generating report..."
 
       File.open options[:output_file], "w" do |f|
         f.puts tracker.report.send(options[:output_format])
       end
-      warn "Report saved in '#{options[:output_file]}'"
+      notify "Report saved in '#{options[:output_file]}'"
     elsif options[:print_report]
-      warn "Generating report..."
+      notify "Generating report..."
 
       puts tracker.report.send(options[:output_format])
     end
@@ -273,11 +276,27 @@ module Brakeman
   #The returned Tracker object from Brakeman.run is used as a starting point
   #for the rescan.
   #
+  #Options may be given as a hash with the same values as Brakeman.run.
+  #Note that these options will be merged into the Tracker.
+  #
   #This method returns a RescanReport object with information about the scan.
   #However, the Tracker object will also be modified as the scan is run.
-  def self.rescan tracker, files
+  def self.rescan tracker, files, options = {}
     require 'brakeman/rescanner'
 
+    tracker.options.merge! options
+
+    @quiet = !!tracker.options[:quiet]
+    @debug = !!tracker.options[:debug]
+
     Rescanner.new(tracker.options, tracker.processor, files).recheck
   end
+
+  def self.notify message
+    $stderr.puts message unless @quiet
+  end
+
+  def self.debug message
+    $stderr.puts message if @debug
+  end
 end
diff --git a/lib/brakeman/call_index.rb b/lib/brakeman/call_index.rb
index bdf338f95d2e742c5868fe7ba6ea360af31c5ee1..b162ad9434bae164047ba0cb28979fab853d97d6 100644
--- a/lib/brakeman/call_index.rb
+++ b/lib/brakeman/call_index.rb
@@ -55,7 +55,7 @@ class Brakeman::CallIndex
     elsif method
       calls = calls_by_method method
     else
-      warn "Invalid arguments to CallCache#find_calls: #{options.inspect}"
+      notify "Invalid arguments to CallCache#find_calls: #{options.inspect}"
     end
 
     return [] if calls.nil?
diff --git a/lib/brakeman/checks.rb b/lib/brakeman/checks.rb
index 9df220e0f790ccb1a3f46c5d6d8d7a0824eb4aff..7dcacb5db567da553674fe5bfcc758fc7b6d455d 100644
--- a/lib/brakeman/checks.rb
+++ b/lib/brakeman/checks.rb
@@ -89,7 +89,7 @@ class Brakeman::Checks
       unless tracker.options[:skip_checks].include? check_name or 
         (tracker.options[:run_checks] and not tracker.options[:run_checks].include? check_name)
 
-        warn " - #{check_name}"
+        Brakeman.notify " - #{check_name}"
 
         check = c.new(tracker)
         check.run_check
@@ -120,7 +120,7 @@ class Brakeman::Checks
       unless tracker.options[:skip_checks].include? check_name or 
         (tracker.options[:run_checks] and not tracker.options[:run_checks].include? check_name)
 
-        warn " - #{check_name}"
+        Brakeman.notify " - #{check_name}"
 
         threads << Thread.new do
           begin
@@ -128,7 +128,7 @@ class Brakeman::Checks
             check.run_check
             check.warnings
           rescue Exception => e
-            warn "[#{check_name}] #{e}"
+            Brakeman.notify "[#{check_name}] #{e}"
             []
           end
         end
@@ -141,7 +141,7 @@ class Brakeman::Checks
 
     threads.each { |t| t.join }
 
-    warn "Checks finished, collecting results..."
+    Brakeman.notify "Checks finished, collecting results..."
 
     #Collect results
     threads.each do |thread|
diff --git a/lib/brakeman/checks/check_cross_site_scripting.rb b/lib/brakeman/checks/check_cross_site_scripting.rb
index 3f7d72a366fcd44696783c1f03be9e67a772950e..42f51de20256cd9de02f9312be02a53e066ee317 100644
--- a/lib/brakeman/checks/check_cross_site_scripting.rb
+++ b/lib/brakeman/checks/check_cross_site_scripting.rb
@@ -59,10 +59,10 @@ class Brakeman::CheckCrossSiteScripting < Brakeman::BaseCheck
     tracker.each_template do |name, template|
       @current_template = template
       template[:outputs].each do |out|
-        debug_info "Checking #{name} for direct XSS"
+        Brakeman.debug "Checking #{name} for direct XSS"
 
         unless check_for_immediate_xss out
-          debug_info "Checking #{name} for indirect XSS"
+          Brakeman.debug "Checking #{name} for indirect XSS"
 
           @matched = false
           @mark = false
diff --git a/lib/brakeman/checks/check_default_routes.rb b/lib/brakeman/checks/check_default_routes.rb
index 7d9ddf9cc50de135b8ccdf64ceab3e408ea6e8f1..f96c61c53c8fcae81fbc95b20771cf6df54ef31b 100644
--- a/lib/brakeman/checks/check_default_routes.rb
+++ b/lib/brakeman/checks/check_default_routes.rb
@@ -15,7 +15,7 @@ class Brakeman::CheckDefaultRoutes < Brakeman::BaseCheck
         :confidence => CONFIDENCE[:high],
         :file => "#{tracker.options[:app_path]}/config/routes.rb"
     else #Report each controller separately
-      debug_info "Checking each controller for default routes"
+      Brakeman.debug "Checking each controller for default routes"
 
       tracker.routes.each do |name, actions|
         if actions.is_a? Array and actions[0] == :allow_all_actions
diff --git a/lib/brakeman/checks/check_evaluation.rb b/lib/brakeman/checks/check_evaluation.rb
index 445261d45d421d2499ba229fa9279cc810528f82..3158d52e6034e29351df5562e8f53300b4aad7fb 100644
--- a/lib/brakeman/checks/check_evaluation.rb
+++ b/lib/brakeman/checks/check_evaluation.rb
@@ -7,10 +7,10 @@ class Brakeman::CheckEvaluation < Brakeman::BaseCheck
 
   #Process calls
   def run_check
-    debug_info "Finding eval-like calls"
+    Brakeman.debug "Finding eval-like calls"
     calls = tracker.find_call :method => [:eval, :instance_eval, :class_eval, :module_eval]
 
-    debug_info "Processing eval-like calls"
+    Brakeman.debug "Processing eval-like calls"
     calls.each do |call|
       process_result call
     end
diff --git a/lib/brakeman/checks/check_execute.rb b/lib/brakeman/checks/check_execute.rb
index 44b990e6fa859970e82297db1bd046cab52d4dd8..736452185e4f214ff4b7b53347d59e0fe40ba051 100644
--- a/lib/brakeman/checks/check_execute.rb
+++ b/lib/brakeman/checks/check_execute.rb
@@ -13,13 +13,13 @@ class Brakeman::CheckExecute < Brakeman::BaseCheck
 
   #Check models, controllers, and views for command injection.
   def run_check
-    debug_info "Finding system calls using ``"
+    Brakeman.debug "Finding system calls using ``"
     check_for_backticks tracker
 
-    debug_info "Finding other system calls"
+    Brakeman.debug "Finding other system calls"
     calls = tracker.find_call :targets => [:IO, :Open3, :Kernel, nil], :methods => [:exec, :popen, :popen3, :syscall, :system]
 
-    debug_info "Processing system calls"
+    Brakeman.debug "Processing system calls"
     calls.each do |result|
       process_result result
     end
diff --git a/lib/brakeman/checks/check_file_access.rb b/lib/brakeman/checks/check_file_access.rb
index e2af71e723b96e735ef2e12893967ff385877b93..48f868267968404a1f3e00f053c30a1893cec5de 100644
--- a/lib/brakeman/checks/check_file_access.rb
+++ b/lib/brakeman/checks/check_file_access.rb
@@ -6,16 +6,16 @@ class Brakeman::CheckFileAccess < Brakeman::BaseCheck
   Brakeman::Checks.add self
 
   def run_check
-    debug_info "Finding possible file access"
+    Brakeman.debug "Finding possible file access"
     methods = tracker.find_call :targets => [:Dir, :File, :IO, :Kernel, :"Net::FTP", :"Net::HTTP", :PStore, :Pathname, :Shell, :YAML], :methods => [:[], :chdir, :chroot, :delete, :entries, :foreach, :glob, :install, :lchmod, :lchown, :link, :load, :load_file, :makedirs, :move, :new, :open, :read, :read_lines, :rename, :rmdir, :safe_unlink, :symlink, :syscopy, :sysopen, :truncate, :unlink]
 
-    debug_info "Finding calls to load()"
+    Brakeman.debug "Finding calls to load()"
     methods.concat tracker.find_call :target => false, :method => :load
 
-    debug_info "Finding calls using FileUtils"
+    Brakeman.debug "Finding calls using FileUtils"
     methods.concat tracker.find_call :target => :FileUtils
 
-    debug_info "Processing found calls"
+    Brakeman.debug "Processing found calls"
     methods.each do |call|
       process_result call
     end
diff --git a/lib/brakeman/checks/check_mail_to.rb b/lib/brakeman/checks/check_mail_to.rb
index 1f55b2d9e0abf26d858e6ad87118cde07ba04836..5a297d5cc7d5d100f26af1d17b4e72731a9989d8 100644
--- a/lib/brakeman/checks/check_mail_to.rb
+++ b/lib/brakeman/checks/check_mail_to.rb
@@ -28,7 +28,7 @@ class Brakeman::CheckMailTo < Brakeman::BaseCheck
   #Check for javascript encoding of mail_to address
   #    mail_to email, name, :encode => :javascript
   def mail_to_javascript?
-    debug_info "Checking calls to mail_to for javascript encoding"
+    Brakeman.debug "Checking calls to mail_to for javascript encoding"
 
     tracker.find_call(:target => false, :method => :mail_to).each do |result|
       call = result[:call]
diff --git a/lib/brakeman/checks/check_mass_assignment.rb b/lib/brakeman/checks/check_mass_assignment.rb
index 3a8e22dfde511cddef28f677a921bbb30873d9d7..ca2c61078f8475de1f497e68c087f71c715f492a 100644
--- a/lib/brakeman/checks/check_mass_assignment.rb
+++ b/lib/brakeman/checks/check_mass_assignment.rb
@@ -21,7 +21,7 @@ class Brakeman::CheckMassAssignment < Brakeman::BaseCheck
 
     @results = Set.new
 
-    debug_info "Finding possible mass assignment calls on #{models.length} models"
+    Brakeman.debug "Finding possible mass assignment calls on #{models.length} models"
     calls = tracker.find_call :chained => true, :targets => models, :methods => [:new,
       :attributes=, 
       :update_attribute, 
@@ -30,7 +30,7 @@ class Brakeman::CheckMassAssignment < Brakeman::BaseCheck
       :create,
       :create!]
 
-    debug_info "Processing possible mass assignment calls"
+    Brakeman.debug "Processing possible mass assignment calls"
     calls.each do |result|
       process_result result
     end
diff --git a/lib/brakeman/checks/check_quote_table_name.rb b/lib/brakeman/checks/check_quote_table_name.rb
index 5770e237dac4f0c817adefac47ce25c637c53141..a817b2169dbe5c0a551c5ddd9fd6d4f72d166c23 100644
--- a/lib/brakeman/checks/check_quote_table_name.rb
+++ b/lib/brakeman/checks/check_quote_table_name.rb
@@ -29,7 +29,7 @@ class Brakeman::CheckQuoteTableName < Brakeman::BaseCheck
   end
 
   def uses_quote_table_name?
-    debug_info "Finding calls to quote_table_name()"
+    Brakeman.debug "Finding calls to quote_table_name()"
 
     not tracker.find_call(:target => false, :method => :quote_table_name).empty?
   end
diff --git a/lib/brakeman/checks/check_redirect.rb b/lib/brakeman/checks/check_redirect.rb
index ef85598464e39dda9024aa7fea9dbd5b04cc1925..ce795ff4053356aacee7a1752079a72082bf26e2 100644
--- a/lib/brakeman/checks/check_redirect.rb
+++ b/lib/brakeman/checks/check_redirect.rb
@@ -9,7 +9,7 @@ class Brakeman::CheckRedirect < Brakeman::BaseCheck
   Brakeman::Checks.add self
 
   def run_check
-    debug_info "Finding calls to redirect_to()"
+    Brakeman.debug "Finding calls to redirect_to()"
 
     @tracker.find_call(:target => false, :method => :redirect_to).each do |res|
       process_result res
@@ -42,7 +42,7 @@ class Brakeman::CheckRedirect < Brakeman::BaseCheck
   #which can be used to enable/disable reporting output of method calls which use
   #user input as arguments.
   def include_user_input? call
-    debug_info "Checking if call includes user input"
+    Brakeman.debug "Checking if call includes user input"
 
     if tracker.options[:ignore_redirect_to_model] and call? call[3][1] and 
       call[3][1][2] == :new and call[3][1][1]
diff --git a/lib/brakeman/checks/check_send_file.rb b/lib/brakeman/checks/check_send_file.rb
index 589a41e79c222aca74e396845c2679d545f26755..7cf05bf2b5bf669de307613e63bf1b4f028089a1 100644
--- a/lib/brakeman/checks/check_send_file.rb
+++ b/lib/brakeman/checks/check_send_file.rb
@@ -6,7 +6,7 @@ class Brakeman::CheckSendFile < Brakeman::CheckFileAccess
   Brakeman::Checks.add self
 
   def run_check
-    debug_info "Finding all calls to send_file()"
+    Brakeman.debug "Finding all calls to send_file()"
 
     methods = tracker.find_call :target => false, :method => :send_file
 
diff --git a/lib/brakeman/checks/check_sql.rb b/lib/brakeman/checks/check_sql.rb
index bcbe32ac42ecf2197c7cedc272745a55c7c4b80d..554e559c9f07172a8a71d20ee98d2f6dd9b126f5 100644
--- a/lib/brakeman/checks/check_sql.rb
+++ b/lib/brakeman/checks/check_sql.rb
@@ -14,7 +14,7 @@ class Brakeman::CheckSQL < Brakeman::BaseCheck
   def run_check
     @rails_version = tracker.config[:rails_version]
 
-    debug_info "Finding possible SQL calls on models"
+    Brakeman.debug "Finding possible SQL calls on models"
     if tracker.options[:rails3]
       calls = tracker.find_call :targets => tracker.models.keys,
         :methods => /^(find.*|first|last|all|where|order|group|having)$/,
@@ -25,16 +25,16 @@ class Brakeman::CheckSQL < Brakeman::BaseCheck
         :chained => true
     end
 
-    debug_info "Finding possible SQL calls with no target"
+    Brakeman.debug "Finding possible SQL calls with no target"
     calls.concat tracker.find_call(:target => nil, :method => /^(find.*|last|first|all|count|sum|average|minumum|maximum|count_by_sql)$/)
 
-    debug_info "Finding possible SQL calls using constantized()"
+    Brakeman.debug "Finding possible SQL calls using constantized()"
     calls.concat tracker.find_call(:method => /^(find.*|last|first|all|count|sum|average|minumum|maximum|count_by_sql)$/).select { |result| constantize_call? result }
 
-    debug_info "Finding calls to named_scope or scope"
+    Brakeman.debug "Finding calls to named_scope or scope"
     calls.concat find_scope_calls
 
-    debug_info "Processing possible SQL calls"
+    Brakeman.debug "Processing possible SQL calls"
     calls.each do |c|
       process_result c
     end
diff --git a/lib/brakeman/checks/check_strip_tags.rb b/lib/brakeman/checks/check_strip_tags.rb
index 214eba787675b5e9ca8c7ac58b621c2bf03a6527..1fdd59311a6596e4a9f2e5517a2a6da7925c6778 100644
--- a/lib/brakeman/checks/check_strip_tags.rb
+++ b/lib/brakeman/checks/check_strip_tags.rb
@@ -23,7 +23,7 @@ class Brakeman::CheckStripTags < Brakeman::BaseCheck
   end
 
   def uses_strip_tags?
-    debug_info "Finding calls to strip_tags()"
+    Brakeman.debug "Finding calls to strip_tags()"
 
     not tracker.find_call(:target => false, :method => :strip_tags).empty?
   end
diff --git a/lib/brakeman/checks/check_translate_bug.rb b/lib/brakeman/checks/check_translate_bug.rb
index fa0040b4ad561924e77ce1edb7de5a252d37a1ca..8b9d8b1d92f7f014ce654315e8443ac39fb2a58e 100644
--- a/lib/brakeman/checks/check_translate_bug.rb
+++ b/lib/brakeman/checks/check_translate_bug.rb
@@ -34,7 +34,7 @@ class Brakeman::CheckTranslateBug < Brakeman::BaseCheck
   end
 
   def uses_translate?
-    debug_info "Finding calls to translate() or t()"
+    Brakeman.debug "Finding calls to translate() or t()"
 
     not tracker.find_call(:target => nil, :methods => [:t, :translate]).empty?
   end
diff --git a/lib/brakeman/checks/check_without_protection.rb b/lib/brakeman/checks/check_without_protection.rb
index fe2c45f2c3ab226cdea643dbbba5e86e816fa2ac..4d5fa14718b14efcfea5d6b6e5ae110ffd51bb8b 100644
--- a/lib/brakeman/checks/check_without_protection.rb
+++ b/lib/brakeman/checks/check_without_protection.rb
@@ -23,7 +23,7 @@ class Brakeman::CheckWithoutProtection < Brakeman::BaseCheck
 
     @results = Set.new
 
-    debug_info "Finding all mass assignments"
+    Brakeman.debug "Finding all mass assignments"
     calls = tracker.find_call :targets => models, :methods => [:new,
       :attributes=, 
       :update_attribute, 
@@ -32,7 +32,7 @@ class Brakeman::CheckWithoutProtection < Brakeman::BaseCheck
       :create,
       :create!]
 
-    debug_info "Processing all mass assignments"
+    Brakeman.debug "Processing all mass assignments"
     calls.each do |result|
       process_result result
     end
diff --git a/lib/brakeman/processors/controller_alias_processor.rb b/lib/brakeman/processors/controller_alias_processor.rb
index 403ec4006e39e9a817b02461136dc7211dac7c5a..952de88ab92390f0dfa4c2126aabf8e8b167b091 100644
--- a/lib/brakeman/processors/controller_alias_processor.rb
+++ b/lib/brakeman/processors/controller_alias_processor.rb
@@ -87,7 +87,7 @@ class Brakeman::ControllerAliasProcessor < Brakeman::AliasProcessor
     method = find_method name, @current_class    
 
     if method.nil?
-      warn "[Notice] Could not find filter #{name}" if @tracker.options[:debug]
+      Brakeman.debug "[Notice] Could not find filter #{name}"
       return
     end
 
@@ -207,7 +207,7 @@ class Brakeman::ControllerAliasProcessor < Brakeman::AliasProcessor
       when :lit, :str
         filter[option] = value[1]
       else
-        warn "[Notice] Unknown before_filter value: #{option} => #{value}" if @tracker.options[:debug]
+        Brakeman.debug "[Notice] Unknown before_filter value: #{option} => #{value}"
       end
     else
       filter[:all] = true
diff --git a/lib/brakeman/processors/controller_processor.rb b/lib/brakeman/processors/controller_processor.rb
index 1a0fb604087c44e3a2a9f4c9eeaaa58f54eea87f..9a3c961aac470e42f79ff40f737b6cc007d3e7c6 100644
--- a/lib/brakeman/processors/controller_processor.rb
+++ b/lib/brakeman/processors/controller_processor.rb
@@ -22,7 +22,7 @@ class Brakeman::ControllerProcessor < Brakeman::BaseProcessor
   #s(:class, NAME, PARENT, s(:scope ...))
   def process_class exp
     if @controller
-      warn "[Notice] Skipping inner class: #{class_name exp[1]}" if @tracker.options[:debug]
+      Brakeman.debug "[Notice] Skipping inner class: #{class_name exp[1]}"
       return ignore
     end
 
@@ -83,7 +83,7 @@ class Brakeman::ControllerProcessor < Brakeman::BaseProcessor
             unless Dir.glob("#{@tracker.options[:app_path]}/app/views/layouts/#{name}.html.{erb,haml}").empty?
               @controller[:layout] = "layouts/#{name}"
             else
-              warn "[Notice] Layout not found: #{name}" if @tracker.options[:debug]
+              Brakeman.debug "[Notice] Layout not found: #{name}"
             end
           elsif sexp? args[-1] and (args[-1][0] == :nil or args[-1][0] == :false)
             #layout :false or layout nil
diff --git a/lib/brakeman/processors/lib/rails2_config_processor.rb b/lib/brakeman/processors/lib/rails2_config_processor.rb
index d12a30a6e5e0d2aaf1b94cd75e07336db3ad0459..400adcbc0d7e354539f422199afaebfbc8875c60 100644
--- a/lib/brakeman/processors/lib/rails2_config_processor.rb
+++ b/lib/brakeman/processors/lib/rails2_config_processor.rb
@@ -37,7 +37,7 @@ class Brakeman::Rails2ConfigProcessor < Brakeman::BaseProcessor
     target = process target if sexp? target
 
     if exp[2] == :gem and exp[3][1][1] == "erubis"
-      warn "[Notice] Using Erubis for ERB templates"
+      Brakeman.notify "[Notice] Using Erubis for ERB templates"
       @tracker.config[:erubis] = true
     end
 
diff --git a/lib/brakeman/processors/lib/render_helper.rb b/lib/brakeman/processors/lib/render_helper.rb
index 77e0d753163c590e89e0f3a3051dae42951ad4e9..a2f4854559c3022cd0a73633f15608c5e2a75a4b 100644
--- a/lib/brakeman/processors/lib/render_helper.rb
+++ b/lib/brakeman/processors/lib/render_helper.rb
@@ -50,7 +50,7 @@ module Brakeman::RenderHelper
     name = name.to_s.gsub(/^\//, "")
     template = @tracker.templates[name.to_sym]
     unless template
-      warn "[Notice] No such template: #{name}" if @tracker.options[:debug]
+      Brakeman.debug "[Notice] No such template: #{name}"
       return 
     end
 
diff --git a/lib/brakeman/processors/model_processor.rb b/lib/brakeman/processors/model_processor.rb
index 7766b48a39f972ca6a0594cd968e38001aea385f..58bc740201614f9853803e5b3d592dea26cf2ec6 100644
--- a/lib/brakeman/processors/model_processor.rb
+++ b/lib/brakeman/processors/model_processor.rb
@@ -19,7 +19,7 @@ class Brakeman::ModelProcessor < Brakeman::BaseProcessor
   #s(:class, NAME, PARENT, s(:scope ...))
   def process_class exp
     if @model
-      warn "[Notice] Skipping inner class: #{class_name exp[1]}" if @tracker.options[:debug]
+      Brakeman.debug "[Notice] Skipping inner class: #{class_name exp[1]}"
       ignore
     else
       @model = { :name => class_name(exp[1]),
diff --git a/lib/brakeman/processors/output_processor.rb b/lib/brakeman/processors/output_processor.rb
index 108ab562ceba0bb284eabe1d73858730489bb54b..c96b482917e6d2ede4e707620259ff27a176294a 100644
--- a/lib/brakeman/processors/output_processor.rb
+++ b/lib/brakeman/processors/output_processor.rb
@@ -19,7 +19,7 @@ class Brakeman::OutputProcessor < Ruby2Ruby
     begin
       super exp if sexp? exp and not exp.empty?
     rescue Exception => e
-      warn "While formatting #{exp}: #{e}\n#{e.backtrace.join("\n")}" if @tracker.options[:debug]
+      Brakeman.debug "While formatting #{exp}: #{e}\n#{e.backtrace.join("\n")}"
     end
   end
 
diff --git a/lib/brakeman/report.rb b/lib/brakeman/report.rb
index 92dda2762af92314a3d1899b4427739b00767963..c29e4d8993a7d248095300b76ef4d66ce8332ccc 100644
--- a/lib/brakeman/report.rb
+++ b/lib/brakeman/report.rb
@@ -83,7 +83,7 @@ class Brakeman::Report
       
      
       tracker.errors.each do |w|
-        p w if tracker.options[:debug]
+        Brakeman.debug w.inspect
 
         if html
           w[:error] = CGI.escapeHTML w[:error]
diff --git a/lib/brakeman/rescanner.rb b/lib/brakeman/rescanner.rb
index a2a81193023bfe927b99f9eb8ff5953375f37d2f..4eec22f9188073123c93592417003edc94ee3508 100644
--- a/lib/brakeman/rescanner.rb
+++ b/lib/brakeman/rescanner.rb
@@ -45,7 +45,7 @@ class Brakeman::Rescanner < Brakeman::Scanner
 
     SCAN_ORDER.each do |type|
       paths_by_type[type].each do |path|
-        warn "Rescanning #{path} as #{type}" if tracker.options[:debug]
+        Brakeman.debug "Rescanning #{path} as #{type}"
 
         if rescan_file path, type
           @changes = true
diff --git a/lib/brakeman/scanner.rb b/lib/brakeman/scanner.rb
index 16d112468252e2b4fc40ceb9fa32ca279fa0393f..7c45d928be2b6e36bd809328babdb3f03dfd9cda 100644
--- a/lib/brakeman/scanner.rb
+++ b/lib/brakeman/scanner.rb
@@ -51,23 +51,23 @@ class Brakeman::Scanner
 
   #Process everything in the Rails application
   def process
-    warn "Processing configuration..."
+    Brakeman.notify "Processing configuration..."
     process_config
-    warn "Processing gems..."
+    Brakeman.notify "Processing gems..."
     process_gems
-    warn "Processing initializers..."
+    Brakeman.notify "Processing initializers..."
     process_initializers
-    warn "Processing libs..."
+    Brakeman.notify "Processing libs..."
     process_libs
-    warn "Processing routes...        "
+    Brakeman.notify "Processing routes...        "
     process_routes
-    warn "Processing templates...     "
+    Brakeman.notify "Processing templates...     "
     process_templates
-    warn "Processing models...        "
+    Brakeman.notify "Processing models...        "
     process_models
-    warn "Processing controllers...   "
+    Brakeman.notify "Processing controllers...   "
     process_controllers
-    warn "Indexing call sites...      "
+    Brakeman.notify "Indexing call sites...      "
     index_call_sites
     tracker
   end
@@ -89,7 +89,7 @@ class Brakeman::Scanner
       (File.exists? "#@path/Gemfile" and File.read("#@path/Gemfile").include? "rails_xss")
 
       tracker.config[:escape_html] = true
-      warn "[Notice] Escaping HTML by default"
+      Brakeman.notify "[Notice] Escaping HTML by default"
     end
   end
 
@@ -99,7 +99,7 @@ class Brakeman::Scanner
     end
 
   rescue Exception => e
-    warn "[Notice] Error while processing config/#{file}"
+    Brakeman.notify "[Notice] Error while processing config/#{file}"
     tracker.error e.exception(e.message + "\nwhile processing Gemfile"), e.backtrace
   end
 
@@ -115,7 +115,7 @@ class Brakeman::Scanner
       end
     end
   rescue Exception => e
-    warn "[Notice] Error while processing Gemfile."
+    Brakeman.notify "[Notice] Error while processing Gemfile."
     tracker.error e.exception(e.message + "\nWhile processing Gemfile"), e.backtrace
   end
 
@@ -144,7 +144,7 @@ class Brakeman::Scanner
   #Adds parsed information to tracker.libs.
   def process_libs
     if options[:skip_libs]
-      warn '[Skipping]'
+      Brakeman.notify '[Skipping]'
       return
     end
 
@@ -153,7 +153,7 @@ class Brakeman::Scanner
     current = 0
 
     lib_files.each do |f|
-      warn "Processing #{f}" if options[:debug]
+      Brakeman.debug "Processing #{f}"
       if @report_progress
         $stderr.print " #{current}/#{total} files processed\r"
         current += 1
@@ -183,11 +183,11 @@ class Brakeman::Scanner
         @processor.process_routes parse_ruby(File.read("#@path/config/routes.rb"))
       rescue Exception => e
         tracker.error e.exception(e.message + "\nWhile processing routes.rb"), e.backtrace
-        warn "[Notice] Error while processing routes - assuming all public controller methods are actions."
+        Brakeman.notify "[Notice] Error while processing routes - assuming all public controller methods are actions."
         options[:assume_all_routes] = true
       end
     else
-      warn "[Notice] No route information found"
+      Brakeman.notify "[Notice] No route information found"
     end
   end
 
@@ -200,7 +200,7 @@ class Brakeman::Scanner
     current = 0
 
     controller_files.each do |f|
-      warn "Processing #{f}" if options[:debug]
+      Brakeman.debug "Processing #{f}"
       if @report_progress
         $stderr.print " #{current}/#{total} files processed\r"
         current += 1
@@ -212,7 +212,7 @@ class Brakeman::Scanner
     current = 0
     total = tracker.controllers.length
 
-    warn "Processing data flow in controllers..."
+    Brakeman.notify "Processing data flow in controllers..."
 
     tracker.controllers.each do |name, controller|
       if @report_progress
@@ -258,7 +258,7 @@ class Brakeman::Scanner
     total = tracker.templates.length
     count = 0
 
-    warn "Processing data flow in templates..."
+    Brakeman.notify "Processing data flow in templates..."
 
     tracker.templates.keys.dup.each do |name|
       if @report_progress