diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index 5fb9ba5f7dd3ac..3ca28ad72c8917 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -36,3 +36,5 @@ a0f7de814ae5c299d6ce99bed5fb308a05d50ba0
 d4e24021d39e1f80f0055b55d91f8d5f22e15084
 7a56c316418980b8a41fcbdc94067b2bda2ad112
 e90282be7ba1bc8e3119f6e1a2c80356ceb3f80a
+26a9e0b4e31f7b5a9cbd755e0a15823a8fa51bae
+2f53985da9ee593fe524d408256835667938c7d7
diff --git a/.github/workflows/zjit-ubuntu.yml b/.github/workflows/zjit-ubuntu.yml
index 040187fca3baf7..7778c449e8e8ea 100644
--- a/.github/workflows/zjit-ubuntu.yml
+++ b/.github/workflows/zjit-ubuntu.yml
@@ -61,6 +61,12 @@ jobs:
             specopts: '-T --zjit-disable-hir-opt -T --zjit-call-threshold=1'
             configure: '--enable-zjit=dev'
 
+            # The optimizer benefits from at least 1 iteration of profiling. Also, many
+            # regression tests in bootstraptest/test_yjit.rb assume call-threshold=2.
+          - test_task: 'btest'
+            run_opts: '--zjit-call-threshold=2'
+            configure: '--enable-zjit=dev'
+
           - test_task: 'zjit-check' # zjit-test + quick feedback of test_zjit.rb
             configure: '--enable-yjit --enable-zjit=dev'
             rust_version: '1.85.0'
diff --git a/.rdoc_options b/.rdoc_options
index b8b511efe67f1e..38dca221112c53 100644
--- a/.rdoc_options
+++ b/.rdoc_options
@@ -11,7 +11,10 @@ rdoc_include:
 exclude:
 - \.gemspec\z
 
+generator_name: aliki
+
 autolink_excluded_words:
+- Box
 - Class
 - Method
 - Module
@@ -23,3 +26,15 @@ autolink_excluded_words:
 - YJIT
 
 canonical_root: https://docs.ruby-lang.org/en/master
+
+footer_content:
+  Ruby:
+    Documentation: index.html
+    Official Website: https://www.ruby-lang.org/
+    Playground: https://ruby.github.io/play-ruby/
+  Resources:
+    GitHub: https://github.com/ruby/ruby
+    Issue Tracker: https://bugs.ruby-lang.org/projects/ruby-master/issues
+    RubyGems: https://rubygems.org/
+  Community:
+    X: https://x.com/rubylangorg
diff --git a/NEWS.md b/NEWS.md
index 9d47bb774ef626..fbbc06713438cd 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -167,7 +167,7 @@ The following bundled gems are promoted from default gems.
 * pstore 0.2.0
 * benchmark 0.5.0
 * logger 1.7.0
-* rdoc 6.15.1
+* rdoc 6.16.0
 * win32ole 1.9.2
 * irb 1.15.3
 * reline 0.6.3
@@ -221,7 +221,7 @@ The following bundled gems are updated.
 * minitest 5.26.2
 * power_assert 3.0.1
 * rake 13.3.1
-* test-unit 3.7.1
+* test-unit 3.7.3
 * rexml 3.4.4
 * net-ftp 0.3.9
 * net-imap 0.5.12
diff --git a/configure.ac b/configure.ac
index 9120fc25ecddf4..22baeabb32ab46 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1749,8 +1749,10 @@ AS_IF([test "$GCC" = yes], [
 	for lib in "" atomic; do
 	    AS_IF([test "$lib" != ""], [
 		AC_CHECK_LIB([atomic], [__atomic_fetch_add_8])
+		unset rb_cv_gcc_atomic_builtins_64
 	    ])
-	    AC_CACHE_CHECK([for 64bit __atomic builtins], [rb_cv_gcc_atomic_builtins_64], [
+	    AC_CACHE_CHECK([for 64bit __atomic builtins${lib:+ with -l$lib}],
+		[rb_cv_gcc_atomic_builtins_64], [
 		AC_LINK_IFELSE([AC_LANG_PROGRAM([[@%:@include <stdint.h>
 			    uint64_t atomic_var;]],
 			    [[
diff --git a/gems/bundled_gems b/gems/bundled_gems
index 2d5c6bdaa1cea1..e1e6b01bfdda10 100644
--- a/gems/bundled_gems
+++ b/gems/bundled_gems
@@ -9,7 +9,7 @@
 minitest            5.26.2  https://github.com/minitest/minitest
 power_assert        3.0.1   https://github.com/ruby/power_assert
 rake                13.3.1  https://github.com/ruby/rake
-test-unit           3.7.1   https://github.com/test-unit/test-unit
+test-unit           3.7.3   https://github.com/test-unit/test-unit
 rexml               3.4.4   https://github.com/ruby/rexml
 rss                 0.3.1   https://github.com/ruby/rss
 net-ftp             0.3.9   https://github.com/ruby/net-ftp
@@ -39,7 +39,7 @@ ostruct             0.6.3   https://github.com/ruby/ostruct
 pstore              0.2.0   https://github.com/ruby/pstore
 benchmark           0.5.0   https://github.com/ruby/benchmark
 logger              1.7.0   https://github.com/ruby/logger
-rdoc                6.15.1  https://github.com/ruby/rdoc
+rdoc                6.16.0  https://github.com/ruby/rdoc
 win32ole            1.9.2   https://github.com/ruby/win32ole
 irb                 1.15.3  https://github.com/ruby/irb
 reline              0.6.3   https://github.com/ruby/reline
diff --git a/imemo.c b/imemo.c
index d83c690ba5ae81..8ec58ae4a92e52 100644
--- a/imemo.c
+++ b/imemo.c
@@ -426,6 +426,13 @@ rb_imemo_mark_and_move(VALUE obj, bool reference_updating)
 
             rb_gc_mark_and_move_ptr(&env->iseq);
 
+            if (VM_ENV_LOCAL_P(env->ep) && VM_ENV_BOXED_P(env->ep)) {
+                const rb_box_t *box = VM_ENV_BOX(env->ep);
+                if (BOX_USER_P(box)) {
+                    rb_gc_mark_and_move((VALUE *)&box->box_object);
+                }
+            }
+
             if (reference_updating) {
                 ((VALUE *)env->ep)[VM_ENV_DATA_INDEX_ENV] = rb_gc_location(env->ep[VM_ENV_DATA_INDEX_ENV]);
             }
diff --git a/test/cgi/test_cgi_escape.rb b/test/cgi/test_cgi_escape.rb
index f6ca658934cdec..73d99e8aacda39 100644
--- a/test/cgi/test_cgi_escape.rb
+++ b/test/cgi/test_cgi_escape.rb
@@ -300,7 +300,7 @@ def setup
       remove_method :escapeHTML
       alias _unescapeHTML unescapeHTML
       remove_method :unescapeHTML
-    end if defined?(CGI::EscapeExt)
+    end if defined?(CGI::EscapeExt) and CGI::EscapeExt.method_defined?(:escapeHTML)
   end
 
   def teardown
@@ -309,7 +309,7 @@ def teardown
       remove_method :_escapeHTML
       alias unescapeHTML _unescapeHTML
       remove_method :_unescapeHTML
-    end if defined?(CGI::EscapeExt)
+    end if defined?(CGI::EscapeExt) and CGI::EscapeExt.method_defined?(:_escapeHTML)
   end
 
   include CGIEscapeTest::UnescapeHTMLTests
diff --git a/test/ruby/test_box.rb b/test/ruby/test_box.rb
index 9b87f9b5bc458a..7023ecab16aa0e 100644
--- a/test/ruby/test_box.rb
+++ b/test/ruby/test_box.rb
@@ -810,4 +810,21 @@ def test_loading_extension_libs_in_main_box
       assert_equal expected, 1
     end;
   end
+
+  def test_mark_box_object_referred_only_from_binding
+    assert_separately([ENV_ENABLE_BOX], __FILE__, __LINE__, "#{<<~"begin;"}\n#{<<~'end;'}", ignore_stderr: true)
+    begin;
+      box = Ruby::Box.new
+      box.eval('class Integer; def +(*)=42; end')
+      b = box.eval('binding')
+      box = nil # remove direct reference to the box
+
+      assert_equal 42, b.eval('1+2')
+
+      GC.stress = true
+      GC.start
+
+      assert_equal 42, b.eval('1+2')
+    end;
+  end
 end
diff --git a/vm.c b/vm.c
index fd8c923649cb65..f9c615c3e23c30 100644
--- a/vm.c
+++ b/vm.c
@@ -3677,6 +3677,13 @@ rb_execution_context_mark(const rb_execution_context_t *ec)
             rb_gc_mark_movable((VALUE)cfp->iseq);
             rb_gc_mark_movable((VALUE)cfp->block_code);
 
+            if (VM_ENV_LOCAL_P(ep) && VM_ENV_BOXED_P(ep)) {
+                const rb_box_t *box = VM_ENV_BOX(ep);
+                if (BOX_USER_P(box)) {
+                    rb_gc_mark_movable(box->box_object);
+                }
+            }
+
             if (!VM_ENV_LOCAL_P(ep)) {
                 const VALUE *prev_ep = VM_ENV_PREV_EP(ep);
                 if (VM_ENV_FLAGS(prev_ep, VM_ENV_FLAG_ESCAPED)) {