diff --git a/lib/bundler/cli.rb b/lib/bundler/cli.rb
index 916ae9bf782..2d63072299a 100644
--- a/lib/bundler/cli.rb
+++ b/lib/bundler/cli.rb
@@ -61,11 +61,6 @@ def initialize(*args)
       end
     end
 
-    def self.deprecated_option(*args, &blk)
-      return if Bundler.feature_flag.forget_cli_options?
-      method_option(*args, &blk)
-    end
-
     check_unknown_options!(:except => [:config, :exec])
     stop_on_unknown_option! :exec
 
@@ -142,7 +137,7 @@ def self.handle_no_command_error(command, has_namespace = $thor_runner)
       Gemfile to a gem with a gemspec, the --gemspec option will automatically add each
       dependency listed in the gemspec file to the newly created Gemfile.
     D
-    deprecated_option "gemspec", :type => :string, :banner => "Use the specified .gemspec to create the Gemfile"
+    method_option "gemspec", :type => :string, :banner => "Use the specified .gemspec to create the Gemfile"
     def init
       require "bundler/cli/init"
       Init.new(options.dup).run
@@ -188,13 +183,13 @@ def remove(*gems)
 
       If the bundle has already been installed, bundler will tell you so and then exit.
     D
-    deprecated_option "binstubs", :type => :string, :lazy_default => "bin", :banner =>
+    method_option "binstubs", :type => :string, :lazy_default => "bin", :banner =>
       "Generate bin stubs for bundled gems to ./bin"
-    deprecated_option "clean", :type => :boolean, :banner =>
+    method_option "clean", :type => :boolean, :banner =>
       "Run bundle clean automatically after install"
-    deprecated_option "deployment", :type => :boolean, :banner =>
+    method_option "deployment", :type => :boolean, :banner =>
       "Install using defaults tuned for deployment environments"
-    deprecated_option "frozen", :type => :boolean, :banner =>
+    method_option "frozen", :type => :boolean, :banner =>
       "Do not allow the Gemfile.lock to be updated after this install"
     method_option "full-index", :type => :boolean, :banner =>
       "Fall back to using the single-file index of all gems"
@@ -204,32 +199,37 @@ def remove(*gems)
       "Specify the number of jobs to run in parallel"
     method_option "local", :type => :boolean, :banner =>
       "Do not attempt to fetch gems remotely and use the gem cache instead"
-    deprecated_option "no-cache", :type => :boolean, :banner =>
+    method_option "no-cache", :type => :boolean, :banner =>
       "Don't update the existing gem cache."
     method_option "redownload", :type => :boolean, :aliases => "--force", :banner =>
       "Force downloading every gem."
-    deprecated_option "no-prune", :type => :boolean, :banner =>
+    method_option "no-prune", :type => :boolean, :banner =>
       "Don't remove stale gems from the cache."
-    deprecated_option "path", :type => :string, :banner =>
+    method_option "path", :type => :string, :banner =>
       "Specify a different path than the system default ($BUNDLE_PATH or $GEM_HOME). Bundler will remember this value for future installs on this machine"
     method_option "quiet", :type => :boolean, :banner =>
       "Only output warnings and errors."
-    deprecated_option "shebang", :type => :string, :banner =>
+    method_option "shebang", :type => :string, :banner =>
       "Specify a different shebang executable name than the default (usually 'ruby')"
     method_option "standalone", :type => :array, :lazy_default => [], :banner =>
       "Make a bundle that can work without the Bundler runtime"
-    deprecated_option "system", :type => :boolean, :banner =>
+    method_option "system", :type => :boolean, :banner =>
       "Install to the system location ($BUNDLE_PATH or $GEM_HOME) even if the bundle was previously installed somewhere else for this application"
     method_option "trust-policy", :alias => "P", :type => :string, :banner =>
       "Gem trust policy (like gem install -P). Must be one of " +
         Bundler.rubygems.security_policy_keys.join("|")
-    deprecated_option "without", :type => :array, :banner =>
+    method_option "without", :type => :array, :banner =>
       "Exclude gems that are part of the specified named group."
-    deprecated_option "with", :type => :array, :banner =>
+    method_option "with", :type => :array, :banner =>
       "Include gems that are part of the specified named group."
     map "i" => "install"
     def install
       SharedHelpers.major_deprecation(2, "The `--force` option has been renamed to `--redownload`") if ARGV.include?("--force")
+
+      %w[clean deployment frozen no-cache no-prune path shebang system without with].each do |option|
+        remembered_flag_deprecation(option)
+      end
+
       require "bundler/cli/install"
       Bundler.settings.temporary(:no_install => false) do
         Install.new(options.dup).run
@@ -786,5 +786,22 @@ def warn_on_outdated_bundler
     rescue RuntimeError
       nil
     end
+
+    def remembered_flag_deprecation(name)
+      option = current_command.options[name]
+      flag_name = option.switch_name
+
+      name_index = ARGV.find {|arg| flag_name == arg }
+      return unless name_index
+
+      value = options[name]
+      value = "#{value.join(" ")}" if option.type == :array
+
+      Bundler::SharedHelpers.major_deprecation 2,\
+        "The `#{flag_name}` flag is deprecated because it relied on being " \
+        "remembered accross bundler invokations, which bundler will no longer " \
+        "do in future versions. Instead please use `bundle config #{name} " \
+        "'#{value}'`, and stop using this flag"
+    end
   end
 end
diff --git a/lib/bundler/dsl.rb b/lib/bundler/dsl.rb
index 6f0d3611605..a53fd7a26f8 100644
--- a/lib/bundler/dsl.rb
+++ b/lib/bundler/dsl.rb
@@ -290,37 +290,21 @@ def add_git_sources
         warn_deprecated_git_source(:github, <<-'RUBY'.strip, 'Change any "reponame" :github sources to "username/reponame".')
 "https://github.com/#{repo_name}.git"
         RUBY
-        # It would be better to use https instead of the git protocol, but this
-        # can break deployment of existing locked bundles when switching between
-        # different versions of Bundler. The change will be made in 2.0, which
-        # does not guarantee compatibility with the 1.x series.
-        #
-        # See https://github.com/bundler/bundler/pull/2569 for discussion
-        #
-        # This can be overridden by adding this code to your Gemfiles:
-        #
-        #   git_source(:github) do |repo_name|
-        #     repo_name = "#{repo_name}/#{repo_name}" unless repo_name.include?("/")
-        #     "https://github.com/#{repo_name}.git"
-        #   end
         repo_name = "#{repo_name}/#{repo_name}" unless repo_name.include?("/")
-        # TODO: 2.0 upgrade this setting to the default
         if Bundler.feature_flag.github_https?
-          Bundler::SharedHelpers.major_deprecation 2, "The `github.https` setting will be removed"
           "https://github.com/#{repo_name}.git"
         else
+          Bundler::SharedHelpers.major_deprecation 2, "Setting `github.https` to false is deprecated and won't be supported in the future."
           "git://github.com/#{repo_name}.git"
         end
       end
 
-      # TODO: 2.0 remove this deprecated git source
       git_source(:gist) do |repo_name|
         warn_deprecated_git_source(:gist, '"https://gist.github.com/#{repo_name}.git"')
 
         "https://gist.github.com/#{repo_name}.git"
       end
 
-      # TODO: 2.0 remove this deprecated git source
       git_source(:bitbucket) do |repo_name|
         warn_deprecated_git_source(:bitbucket, <<-'RUBY'.strip)
 user_name, repo_name = repo_name.split("/")
@@ -488,7 +472,6 @@ def check_primary_source_safety(source_list)
     end
 
     def warn_deprecated_git_source(name, replacement, additional_message = nil)
-      # TODO: 2.0 remove deprecation
       additional_message &&= " #{additional_message}"
       replacement = if replacement.count("\n").zero?
         "{|repo_name| #{replacement} }"
@@ -496,8 +479,8 @@ def warn_deprecated_git_source(name, replacement, additional_message = nil)
         "do |repo_name|\n#{replacement.to_s.gsub(/^/, "      ")}\n    end"
       end
 
-      Bundler::SharedHelpers.major_deprecation 2, <<-EOS
-The :#{name} git source is deprecated, and will be removed in Bundler 2.0.#{additional_message} Add this code to the top of your Gemfile to ensure it continues to work:
+      Bundler::SharedHelpers.major_deprecation 3, <<-EOS
+The :#{name} git source is deprecated, and will be removed in Bundler 3.0.#{additional_message} Add this code to the top of your Gemfile to ensure it continues to work:
 
     git_source(:#{name}) #{replacement}
 
diff --git a/lib/bundler/feature_flag.rb b/lib/bundler/feature_flag.rb
index 0adbd9190f5..aafd37f7663 100644
--- a/lib/bundler/feature_flag.rb
+++ b/lib/bundler/feature_flag.rb
@@ -38,7 +38,7 @@ def self.settings_method(name, key, &default)
     settings_flag(:deployment_means_frozen) { bundler_2_mode? }
     settings_flag(:disable_multisource) { bundler_2_mode? }
     settings_flag(:error_on_stderr) { bundler_2_mode? }
-    settings_flag(:forget_cli_options) { bundler_2_mode? }
+    settings_flag(:forget_cli_options) { bundler_3_mode? }
     settings_flag(:global_path_appends_ruby_scope) { bundler_2_mode? }
     settings_flag(:global_gem_cache) { bundler_2_mode? }
     settings_flag(:init_gems_rb) { bundler_2_mode? }
@@ -50,11 +50,11 @@ def self.settings_method(name, key, &default)
     settings_flag(:prefer_gems_rb) { bundler_2_mode? }
     settings_flag(:print_only_version_number) { bundler_2_mode? }
     settings_flag(:setup_makes_kernel_gem_public) { !bundler_2_mode? }
-    settings_flag(:skip_default_git_sources) { bundler_2_mode? }
+    settings_flag(:skip_default_git_sources) { bundler_3_mode? }
     settings_flag(:specific_platform) { bundler_2_mode? }
     settings_flag(:suppress_install_using_messages) { bundler_2_mode? }
     settings_flag(:unlock_source_unlocks_spec) { !bundler_2_mode? }
-    settings_flag(:update_requires_all_flag) { bundler_2_mode? }
+    settings_flag(:update_requires_all_flag) { bundler_3_mode? }
     settings_flag(:use_gem_version_promoter_for_major_updates) { bundler_2_mode? }
     settings_flag(:viz_command) { !bundler_2_mode? }
 
diff --git a/lib/bundler/settings.rb b/lib/bundler/settings.rb
index ff9a5f57af2..284b9628336 100644
--- a/lib/bundler/settings.rb
+++ b/lib/bundler/settings.rb
@@ -35,6 +35,7 @@ class Settings
       frozen
       gem.coc
       gem.mit
+      github.https
       global_path_appends_ruby_scope
       global_gem_cache
       ignore_messages
@@ -115,11 +116,19 @@ def set_command_option(key, value)
           "bundle config set #{key} #{Array(value).join(":")}"
         end
 
-        Bundler::SharedHelpers.major_deprecation 2,\
-          "flags passed to commands " \
-          "will no longer be automatically remembered. Instead please set flags " \
-          "you want remembered between commands using `bundle config set " \
-          "<setting name> <setting value>`, i.e. `#{command}`"
+        unless Bundler.settings[:forget_cli_options] == false
+          Bundler::SharedHelpers.major_deprecation 3,\
+            "flags passed to commands " \
+            "will no longer be automatically remembered. Instead please set flags " \
+            "you want remembered between commands using `bundle config set " \
+            "<setting name> <setting value>`, i.e. `#{command}`. Once you are " \
+            "ready for the new behavior, use `bundle config set forget_cli_options " \
+            "true` to get rid of this message. Or if you want to get rid of " \
+            "this message and stick with the old behavior for now, run " \
+            "`bundle config set forget_cli_options false`, but keep in mind " \
+            "that this behavior will be fully removed in future versions of " \
+            "bundler."
+        end
 
         set_local(key, value)
       end
diff --git a/lib/bundler/shared_helpers.rb b/lib/bundler/shared_helpers.rb
index 996f7b3fd40..cf53c1acbcb 100644
--- a/lib/bundler/shared_helpers.rb
+++ b/lib/bundler/shared_helpers.rb
@@ -157,11 +157,13 @@ def print_major_deprecations!
       multiple_gemfiles = search_up(".") do |dir|
         gemfiles = gemfile_names.select {|gf| File.file? File.expand_path(gf, dir) }
         next if gemfiles.empty?
-        break false if gemfiles.size == 1
+        break gemfiles.size != 1
       end
-      return unless multiple_gemfiles && Bundler.bundler_major_version == 1
-      Bundler::SharedHelpers.major_deprecation 2, \
-        "gems.rb and gems.locked will be preferred to Gemfile and Gemfile.lock."
+
+      return unless multiple_gemfiles
+
+      Bundler.ui.warn \
+        "Multiple gemfiles (gems.rb and Gemfile) detected. Make sure you remove Gemfile and Gemfile.lock since bundler will ignore them."
     end
 
     def trap(signal, override = false, &block)
diff --git a/spec/bundler/dsl_spec.rb b/spec/bundler/dsl_spec.rb
index ce0544a5732..8d61ef4540a 100644
--- a/spec/bundler/dsl_spec.rb
+++ b/spec/bundler/dsl_spec.rb
@@ -28,7 +28,7 @@
     context "github_https feature flag" do
       it "is true when github.https is true" do
         bundle "config set github.https true"
-        expect(Bundler.feature_flag.github_https?).to eq "true"
+        expect(Bundler.feature_flag.github_https?).to eq true
       end
     end
 
@@ -44,7 +44,7 @@
 
       it "converts :github to :git" do
         subject.gem("sparks", :github => "indirect/sparks")
-        github_uri = "git://github.com/indirect/sparks.git"
+        github_uri = "https://github.com/indirect/sparks.git"
         expect(subject.dependencies.first.source.uri).to eq(github_uri)
       end
 
@@ -62,7 +62,7 @@
 
       it "converts 'rails' to 'rails/rails'" do
         subject.gem("rails", :github => "rails")
-        github_uri = "git://github.com/rails/rails.git"
+        github_uri = "https://github.com/rails/rails.git"
         expect(subject.dependencies.first.source.uri).to eq(github_uri)
       end
 
@@ -79,7 +79,7 @@
       end
     end
 
-    context "default git sources", :bundler => "2" do
+    context "default git sources", :bundler => "3" do
       it "has none" do
         expect(subject.instance_variable_get(:@git_sources)).to eq({})
       end
@@ -245,7 +245,7 @@
     #   gem 'spree_api'
     #   gem 'spree_backend'
     # end
-    describe "#github", :bundler => "< 2" do
+    describe "#github", :bundler => "< 3" do
       it "from github" do
         spree_gems = %w[spree_core spree_api spree_backend]
         subject.github "spree" do
@@ -253,12 +253,12 @@
         end
 
         subject.dependencies.each do |d|
-          expect(d.source.uri).to eq("git://github.com/spree/spree.git")
+          expect(d.source.uri).to eq("https://github.com/spree/spree.git")
         end
       end
     end
 
-    describe "#github", :bundler => "2" do
+    describe "#github", :bundler => "3" do
       it "from github" do
         expect do
           spree_gems = %w[spree_core spree_api spree_backend]
diff --git a/spec/other/major_deprecation_spec.rb b/spec/other/major_deprecation_spec.rb
index ef51112d720..463c907eeae 100644
--- a/spec/other/major_deprecation_spec.rb
+++ b/spec/other/major_deprecation_spec.rb
@@ -1,8 +1,7 @@
 # frozen_string_literal: true
 
-RSpec.describe "major deprecations", :bundler => "< 2" do
+RSpec.describe "major deprecations" do
   let(:warnings) { last_command.bundler_err } # change to err in 2.0
-  let(:warnings_without_version_messages) { warnings.gsub(/#{Spec::Matchers::MAJOR_DEPRECATION}Bundler will only support ruby >= .*/, "") }
 
   before do
     create_file "gems.rb", <<-G
@@ -35,7 +34,7 @@
     describe "bundle update --quiet" do
       it "does not print any deprecations" do
         bundle :update, :quiet => true
-        expect(warnings_without_version_messages).not_to have_major_deprecation
+        expect(warnings).not_to have_major_deprecation
       end
     end
 
@@ -52,7 +51,7 @@
 
       it "does not warn when --all is passed" do
         bundle! "update --all"
-        expect(warnings_without_version_messages).not_to have_major_deprecation
+        expect(warnings).not_to have_major_deprecation
       end
     end
 
@@ -68,7 +67,7 @@
     end
   end
 
-  context "when bundle is run" do
+  context "when bundle install is run" do
     it "should not warn about gems.rb" do
       create_file "gems.rb", <<-G
         source "file://#{gem_repo1}"
@@ -76,22 +75,22 @@
       G
 
       bundle :install
-      expect(warnings_without_version_messages).not_to have_major_deprecation
+      expect(warnings).not_to have_major_deprecation
     end
 
-    it "should print a Gemfile deprecation warning" do
+    it "should print a Gemfile deprecation warning when both types present" do
       create_file "gems.rb"
       install_gemfile! <<-G
         source "file://#{gem_repo1}"
         gem "rack"
       G
-      expect(the_bundle).to include_gem "rack 1.0"
+      expect(the_bundle).not_to include_gem "rack 1.0"
 
-      expect(warnings).to have_major_deprecation a_string_including("gems.rb and gems.locked will be preferred to Gemfile and Gemfile.lock.")
+      expect(warnings).to have_major_deprecation("Multiple gemfiles (gems.rb and Gemfile) detected. Make sure you remove Gemfile and Gemfile.lock since bundler will ignore them.")
     end
 
     context "with flags" do
-      it "should print a deprecation warning about autoremembering flags" do
+      it "should print a deprecation warning about autoremembering flags", :bundler => "3" do
         install_gemfile <<-G, :path => "vendor/bundle"
           source "file://#{gem_repo1}"
           gem "rack"
@@ -101,6 +100,34 @@
           "flags passed to commands will no longer be automatically remembered."
         )
       end
+
+      {
+        :clean => true,
+        :deployment => true,
+        :frozen => true,
+        :"no-cache" => true,
+        :"no-prune" => true,
+        :path => "vendor/bundle",
+        :shebang => "ruby27",
+        :system => true,
+        :without => "development",
+        :with => "development",
+      }.each do |name, value|
+        flag_name = "--#{name}"
+
+        context "with the #{flag_name} flag" do
+          it "should print a deprecation warning" do
+            bundle "install #{flag_name} #{value}"
+
+            expect(warnings).to have_major_deprecation(
+              "The `#{flag_name}` flag is deprecated because it relied on " \
+              "being remembered accross bundler invokations, which bundler " \
+              "will no longer do in future versions. Instead please use " \
+              "`bundle config #{name} '#{value}'`, and stop using this flag"
+            )
+          end
+        end
+      end
     end
   end
 
@@ -122,7 +149,7 @@
         Bundler.setup
       RUBY
 
-      expect(warnings_without_version_messages).to have_major_deprecation("gems.rb and gems.locked will be preferred to Gemfile and Gemfile.lock.")
+      expect(warnings).to include("Multiple gemfiles (gems.rb and Gemfile) detected. Make sure you remove Gemfile and Gemfile.lock since bundler will ignore them.")
     end
   end
 
@@ -146,27 +173,31 @@
     end
 
     context "with github gems" do
-      it "warns about the https change" do
-        msg = <<-EOS
-The :github git source is deprecated, and will be removed in Bundler 2.0. Change any "reponame" :github sources to "username/reponame". Add this code to the top of your Gemfile to ensure it continues to work:
+      let(:msg) do
+        <<-EOS
+The :github git source is deprecated, and will be removed in Bundler 3.0. Change any "reponame" :github sources to "username/reponame". Add this code to the top of your Gemfile to ensure it continues to work:
 
     git_source(:github) {|repo_name| "https://github.com/\#{repo_name}.git" }
 
         EOS
-        expect(Bundler::SharedHelpers).to receive(:major_deprecation).with(2, msg)
-        subject.gem("sparks", :github => "indirect/sparks")
       end
 
-      it "upgrades to https on request" do
-        Bundler.settings.temporary "github.https" => true
-        msg = <<-EOS
-The :github git source is deprecated, and will be removed in Bundler 2.0. Change any "reponame" :github sources to "username/reponame". Add this code to the top of your Gemfile to ensure it continues to work:
+      it "warns about future removal" do
+        expect(Bundler::SharedHelpers).to receive(:major_deprecation).with(3, msg)
+        subject.gem("sparks", :github => "indirect/sparks")
+      end
 
-    git_source(:github) {|repo_name| "https://github.com/\#{repo_name}.git" }
+      it "downgrades to http on request" do
+        Bundler.settings.temporary "github.https" => false
+        expect(Bundler::SharedHelpers).to receive(:major_deprecation).with(3, msg)
+        expect(Bundler::SharedHelpers).to receive(:major_deprecation).with(2, "Setting `github.https` to false is deprecated and won't be supported in the future.")
+        subject.gem("sparks", :github => "indirect/sparks")
+        github_uri = "git://github.com/indirect/sparks.git"
+        expect(subject.dependencies.first.source.uri).to eq(github_uri)
+      end
 
-        EOS
-        expect(Bundler::SharedHelpers).to receive(:major_deprecation).with(2, msg)
-        expect(Bundler::SharedHelpers).to receive(:major_deprecation).with(2, "The `github.https` setting will be removed")
+      it "uses https by default" do
+        expect(Bundler::SharedHelpers).to receive(:major_deprecation).with(3, msg)
         subject.gem("sparks", :github => "indirect/sparks")
         github_uri = "https://github.com/indirect/sparks.git"
         expect(subject.dependencies.first.source.uri).to eq(github_uri)
@@ -177,7 +208,7 @@
       it "warns about removal" do
         allow(Bundler.ui).to receive(:deprecate)
         msg = <<-EOS
-The :bitbucket git source is deprecated, and will be removed in Bundler 2.0. Add this code to the top of your Gemfile to ensure it continues to work:
+The :bitbucket git source is deprecated, and will be removed in Bundler 3.0. Add this code to the top of your Gemfile to ensure it continues to work:
 
     git_source(:bitbucket) do |repo_name|
       user_name, repo_name = repo_name.split("/")
@@ -186,7 +217,7 @@
     end
 
         EOS
-        expect(Bundler::SharedHelpers).to receive(:major_deprecation).with(2, msg)
+        expect(Bundler::SharedHelpers).to receive(:major_deprecation).with(3, msg)
         subject.gem("not-really-a-gem", :bitbucket => "mcorp/flatlab-rails")
       end
     end
@@ -195,10 +226,10 @@
       it "warns about removal" do
         allow(Bundler.ui).to receive(:deprecate)
         msg = "The :gist git source is deprecated, and will be removed " \
-          "in Bundler 2.0. Add this code to the top of your Gemfile to ensure it " \
+          "in Bundler 3.0. Add this code to the top of your Gemfile to ensure it " \
           "continues to work:\n\n    git_source(:gist) {|repo_name| " \
           "\"https://gist.github.com/\#{repo_name}.git\" }\n\n"
-        expect(Bundler::SharedHelpers).to receive(:major_deprecation).with(2, msg)
+        expect(Bundler::SharedHelpers).to receive(:major_deprecation).with(3, msg)
         subject.gem("not-really-a-gem", :gist => "1234")
       end
     end
diff --git a/spec/quality_spec.rb b/spec/quality_spec.rb
index 8bdef33a79f..60de02d5c59 100644
--- a/spec/quality_spec.rb
+++ b/spec/quality_spec.rb
@@ -172,6 +172,7 @@ def check_for_specific_pronouns(filename)
       forget_cli_options
       gem.coc
       gem.mit
+      github.https
       inline
       lockfile_uses_separate_rubygems_sources
       use_gem_version_promoter_for_major_updates