Add back app.set, but mark as deprecated

middleman-core/features/extension_api_deprecations.feature

@@ -0,0 +1,10 @@
+Feature: Extension author could use some hooks
+
+  Scenario: When build
+    Given a fixture app "extension-api-deprecations-app"
+    When I run `middleman build`
+    Then the exit status should be 0
+    And the output should contain "`set :layout` is deprecated"
+    And the file "build/index.html" should contain "In Index"
+    And the file "build/index.html" should not contain "In Layout"
+

middleman-core/fixtures/extension-api-deprecations-app/config.rb

@@ -0,0 +1,11 @@
+class LayoutDisabler < Middleman::Extension
+  def initialize(app, options_hash = {}, &block)
+    super
+
+    app.set :layout, false
+  end
+end
+
+::Middleman::Extensions.register(:layout_disabler, LayoutDisabler)
+
+activate :layout_disabler

middleman-core/fixtures/extension-api-deprecations-app/source/index.html.erb

@@ -0,0 +1 @@
+In Index

middleman-core/fixtures/extension-api-deprecations-app/source/layouts/layout.erb

@@ -0,0 +1,3 @@
+In Layout
+
+<%= yield %>

middleman-core/lib/middleman-core/application.rb

@@ -391,6 +391,21 @@ module Middleman
       execute_callbacks(:before_shutdown)
     end
 
+
+    # Set attributes (global variables)
+    #
+    # @deprecated Prefer accessing settings through "config".
+    #
+    # @param [Symbol] key Name of the attribue
+    # @param value Attribute value
+    # @return [void]
+    def set(key, value=nil, &block)
+      logger.warn "Warning: `set :#{key}` is deprecated. Use `config[:#{key}] =` instead."
+
+      value = block if block_given?
+      config[key] = value
+    end
+
     # Work around this bug: http://bugs.ruby-lang.org/issues/4521
     # where Ruby will call to_s/inspect while printing exception
     # messages, which can take a long time (minutes at full CPU)