diff --git a/docs/package.json b/docs/package.json
index b0d43f02b9..bf6f37615f 100644
--- a/docs/package.json
+++ b/docs/package.json
@@ -13,7 +13,7 @@
     "spellcheck": "cspell --config ./cspell.config.js src"
   },
   "dependencies": {
-    "@shikijs/vitepress-twoslash": "^2.1.0",
+    "@shikijs/vitepress-twoslash": "^4.0.0",
     "@sourceacademy/bundle-curve": "workspace:^",
     "@sourceacademy/bundle-rune": "workspace:^",
     "@sourceacademy/bundle-sound": "workspace:^",
diff --git a/lib/markdown-tree/package.json b/lib/markdown-tree/package.json
index 4c0fac2cb1..d56f71cb27 100644
--- a/lib/markdown-tree/package.json
+++ b/lib/markdown-tree/package.json
@@ -8,7 +8,7 @@
     "@sourceacademy/modules-buildtools": "workspace:^",
     "@sourceacademy/modules-repotools": "workspace:^",
     "@types/markdown-it": "^14.1.2",
-    "shiki": "^2.1.0",
+    "shiki": "^4.0.0",
     "typescript": "^6.0.2"
   },
   "exports": {
@@ -22,7 +22,7 @@
     "shiki": ">=2"
   },
   "dependencies": {
-    "@shikijs/themes": "^2.1.0",
+    "@shikijs/themes": "^4.0.0",
     "es-toolkit": "^1.44.0",
     "yaml": "^2.8.0"
   },
diff --git a/yarn.lock b/yarn.lock
index 62b60f4254..e47bd832bc 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -665,6 +665,13 @@ __metadata:
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+"@babel/helper-string-parser@npm:^7.29.7":
+  version: 7.29.7
+  resolution: "@babel/helper-string-parser@npm:7.29.7"
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+
 "@babel/helper-validator-identifier@npm:^7.28.5":
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   resolution: "@babel/helper-validator-identifier@npm:7.28.5"
@@ -672,6 +679,13 @@ __metadata:
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+"@babel/helper-validator-identifier@npm:^7.29.7":
+  version: 7.29.7
+  resolution: "@babel/helper-validator-identifier@npm:7.29.7"
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+  linkType: hard
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 "@babel/helper-validator-option@npm:^7.27.1":
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   resolution: "@babel/helper-validator-option@npm:7.27.1"
@@ -711,6 +725,17 @@ __metadata:
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+"@babel/parser@npm:^7.29.7":
+  version: 7.29.7
+  resolution: "@babel/parser@npm:7.29.7"
+  dependencies:
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+  bin:
+    parser: ./bin/babel-parser.js
+  checksum: 10c0/65133038f80b54a714d6027cb77cee3f9a6b5c4c6842ce674301e13947cbcbfa8055e63acaf1b84c085d34226a14425b2c2b97b829e0e226d2e8f1299942a51d
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+
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   resolution: "@babel/plugin-syntax-async-generators@npm:7.8.4"
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+"@babel/types@npm:^7.29.7":
+  version: 7.29.7
+  resolution: "@babel/types@npm:7.29.7"
+  dependencies:
+    "@babel/helper-string-parser": "npm:^7.29.7"
+    "@babel/helper-validator-identifier": "npm:^7.29.7"
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+  languageName: node
+  linkType: hard
+
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   resolution: "@bcoe/v8-coverage@npm:1.0.2"
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-  resolution: "@shikijs/core@npm:4.0.2"
+"@shikijs/core@npm:4.3.0":
+  version: 4.3.0
+  resolution: "@shikijs/core@npm:4.3.0"
   dependencies:
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-    "@shikijs/types": "npm:4.0.2"
+    "@shikijs/primitive": "npm:4.3.0"
+    "@shikijs/types": "npm:4.3.0"
     "@shikijs/vscode-textmate": "npm:^10.0.2"
     "@types/hast": "npm:^3.0.4"
     hast-util-to-html: "npm:^9.0.5"
-  checksum: 10c0/0a8c56d50b2f67334e5e128b89f1e85844f60ae1dfbd4171e6e92242398678f6eaf91cd02f8418ac4abf4d81774e0ec9a83274a2e3f609c410e577520eadb0f5
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+  version: 4.3.0
+  resolution: "@shikijs/engine-javascript@npm:4.3.0"
+  dependencies:
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+    "@shikijs/vscode-textmate": "npm:^10.0.2"
+    oniguruma-to-es: "npm:^4.3.6"
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+  resolution: "@shikijs/engine-oniguruma@npm:4.3.0"
+  dependencies:
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+    "@shikijs/vscode-textmate": "npm:^10.0.2"
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+  languageName: node
+  linkType: hard
+
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   resolution: "@shikijs/engine-oniguruma@npm:3.22.0"
@@ -3742,6 +3798,15 @@ __metadata:
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+"@shikijs/langs@npm:4.3.0":
+  version: 4.3.0
+  resolution: "@shikijs/langs@npm:4.3.0"
+  dependencies:
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+  languageName: node
+  linkType: hard
+
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   resolution: "@shikijs/langs@npm:3.22.0"
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-  version: 4.0.2
-  resolution: "@shikijs/primitive@npm:4.0.2"
+"@shikijs/primitive@npm:4.3.0":
+  version: 4.3.0
+  resolution: "@shikijs/primitive@npm:4.3.0"
   dependencies:
-    "@shikijs/types": "npm:4.0.2"
+    "@shikijs/types": "npm:4.3.0"
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     "@types/hast": "npm:^3.0.4"
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+  checksum: 10c0/ce34e6bc917bd73e3aed0591c3ff2d7f73069c5dc1b1eb2cff3f5a7407340518568e3b2a43eb3dac6854dfc7cf146e60c7868de0f0fe68edb5873ba633a4c6a2
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   resolution: "@shikijs/themes@npm:2.5.0"
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+"@shikijs/themes@npm:4.3.0, @shikijs/themes@npm:^4.0.0":
+  version: 4.3.0
+  resolution: "@shikijs/themes@npm:4.3.0"
+  dependencies:
+    "@shikijs/types": "npm:4.3.0"
+  checksum: 10c0/5c63942de6eabf6c6e72c801000cbf4042222d855ee94c0cd3e4b2b62c70083db47d6b542f9c789d9bc62552be139b436a4db270bb73cf1206f1e63802521a4b
+  languageName: node
+  linkType: hard
+
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   resolution: "@shikijs/themes@npm:3.22.0"
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-  version: 4.0.2
-  resolution: "@shikijs/twoslash@npm:4.0.2"
+"@shikijs/twoslash@npm:4.3.0":
+  version: 4.3.0
+  resolution: "@shikijs/twoslash@npm:4.3.0"
   dependencies:
-    "@shikijs/core": "npm:4.0.2"
-    "@shikijs/types": "npm:4.0.2"
-    twoslash: "npm:^0.3.6"
+    "@shikijs/core": "npm:4.3.0"
+    "@shikijs/types": "npm:4.3.0"
+    twoslash: "npm:^0.3.9"
   peerDependencies:
     typescript: ">=5.5.0"
-  checksum: 10c0/a3bec3f3b8596cb2d189a1001ff3a6721b961deca0b321e0b9892381e0bb0ecb5032d265b4e82da9b82fe78d2c8efa0e1d940e38134cb66cbaa098909094ecd9
+  checksum: 10c0/d9c2e6c8a65ab471899deec004ac00d24aa374c6d33f2ab54f4d7f361f5d01a39a63128b834f0339d3a2017b06ffa9822e8508ddc101bb8f21bf4c551c323f1d
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-"@shikijs/types@npm:4.0.2":
-  version: 4.0.2
-  resolution: "@shikijs/types@npm:4.0.2"
+"@shikijs/types@npm:4.3.0":
+  version: 4.3.0
+  resolution: "@shikijs/types@npm:4.3.0"
   dependencies:
     "@shikijs/vscode-textmate": "npm:^10.0.2"
     "@types/hast": "npm:^3.0.4"
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+  checksum: 10c0/b2f461511cefe20ba25978dfa2462246db7053d9fd03732e6c969c30fda413db9109e635aea5e58d56ab3946caa0d0bd6fdb043240a29c6f4ad5a4996442a823
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-  resolution: "@shikijs/vitepress-twoslash@npm:2.5.0"
+"@shikijs/vitepress-twoslash@npm:^4.0.0":
+  version: 4.3.0
+  resolution: "@shikijs/vitepress-twoslash@npm:4.3.0"
   dependencies:
-    "@shikijs/twoslash": "npm:"
+    "@shikijs/twoslash": "npm:4.3.0"
     floating-vue: "npm:^5.2.2"
-    mdast-util-from-markdown: "npm:^2.0.2"
+    lz-string: "npm:^1.5.0"
+    magic-string: "npm:^0.30.21"
+    markdown-it: "npm:^14.2.0"
+    mdast-util-from-markdown: "npm:^2.0.3"
     mdast-util-gfm: "npm:^3.1.0"
-    mdast-util-to-hast: "npm:^13.2.0"
-    shiki: "npm:2.5.0"
-    twoslash: "npm:^0.2.12"
-    twoslash-vue: "npm:^0.2.12"
-    vue: "npm:^3.5.13"
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+    mdast-util-to-hast: "npm:^13.2.1"
+    ohash: "npm:^2.0.11"
+    shiki: "npm:4.3.0"
+    twoslash: "npm:^0.3.9"
+    twoslash-vue: "npm:^0.3.9"
+    vue: "npm:^3.5.38"
+  checksum: 10c0/057bce4fb2985c59afa9e8568f2189dee1eb0e2a69be1dfe4d05d785fa789fdbfb0e316145d1ed7c33cd4a310716059bb5c468b66c3ae01fb695256c8daa5524
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   resolution: "@sourceacademy/markdown-plugin-directory-tree@workspace:lib/markdown-tree"
   dependencies:
-    "@shikijs/themes": "npm:^2.1.0"
+    "@shikijs/themes": "npm:^4.0.0"
     "@sourceacademy/modules-buildtools": "workspace:^"
     "@sourceacademy/modules-repotools": "workspace:^"
     "@types/markdown-it": "npm:^14.1.2"
     es-toolkit: "npm:^1.44.0"
-    shiki: "npm:^2.1.0"
+    shiki: "npm:^4.0.0"
     typescript: "npm:^6.0.2"
     yaml: "npm:^2.8.0"
   peerDependencies:
@@ -4400,7 +4478,7 @@ __metadata:
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   resolution: "@sourceacademy/modules-docserver@workspace:docs"
   dependencies:
-    "@shikijs/vitepress-twoslash": "npm:^2.1.0"
+    "@shikijs/vitepress-twoslash": "npm:^4.0.0"
     "@sourceacademy/bundle-curve": "workspace:^"
     "@sourceacademy/bundle-rune": "workspace:^"
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   resolution: "@volar/language-core@npm:2.4.28"
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+"@vue/compiler-core@npm:3.5.39":
+  version: 3.5.39
+  resolution: "@vue/compiler-core@npm:3.5.39"
+  dependencies:
+    "@babel/parser": "npm:^7.29.7"
+    "@vue/shared": "npm:3.5.39"
+    entities: "npm:^7.0.1"
+    estree-walker: "npm:^2.0.2"
+    source-map-js: "npm:^1.2.1"
+  checksum: 10c0/97592f35505713b2024e92cf58806db0abe5519a1462c06269f71cb8ddcefa9ce680d192ddfa3ef456c741c91fb3955f2e414a27dd40ad1e145b8f051b389988
+  languageName: node
+  linkType: hard
+
 "@vue/compiler-dom@npm:3.5.17":
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   resolution: "@vue/compiler-dom@npm:3.5.17"
@@ -6288,6 +6379,16 @@ __metadata:
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   linkType: hard
 
+"@vue/compiler-dom@npm:3.5.39":
+  version: 3.5.39
+  resolution: "@vue/compiler-dom@npm:3.5.39"
+  dependencies:
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+  checksum: 10c0/0e3fb865209b918bb59d19d1b9d8349c6474dcae977fb74a264481d9af45f65632752c7ae42a7dd552e9b6de0612678bef4db713a5f8afacaab12e17b1c5bbb6
+  languageName: node
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@@ -6315,6 +6416,23 @@ __metadata:
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+  version: 3.5.39
+  resolution: "@vue/compiler-sfc@npm:3.5.39"
+  dependencies:
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+    "@vue/compiler-dom": "npm:3.5.39"
+    "@vue/compiler-ssr": "npm:3.5.39"
+    "@vue/shared": "npm:3.5.39"
+    estree-walker: "npm:^2.0.2"
+    magic-string: "npm:^0.30.21"
+    postcss: "npm:^8.5.15"
+    source-map-js: "npm:^1.2.1"
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-  version: 2.7.16
-  resolution: "@vue/compiler-vue2@npm:2.7.16"
+"@vue/compiler-ssr@npm:3.5.39":
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+  resolution: "@vue/compiler-ssr@npm:3.5.39"
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+    "@vue/shared": "npm:3.5.39"
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-  resolution: "@vue/language-core@npm:2.1.10"
+"@vue/language-core@npm:^3.2.6":
+  version: 3.3.5
+  resolution: "@vue/language-core@npm:3.3.5"
   dependencies:
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+    "@volar/language-core": "npm:2.4.28"
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     "@vue/shared": "npm:^3.5.0"
-    alien-signals: "npm:^0.2.0"
-    minimatch: "npm:^9.0.3"
+    alien-signals: "npm:^3.2.0"
     muggle-string: "npm:^0.4.1"
     path-browserify: "npm:^1.0.1"
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+    picomatch: "npm:^4.0.4"
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@@ -6398,6 +6510,15 @@ __metadata:
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+    mdurl: "npm:^2.0.0"
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+    micromark-util-decode-numeric-character-reference: "npm:^2.0.0"
+    micromark-util-decode-string: "npm:^2.0.0"
+    micromark-util-normalize-identifier: "npm:^2.0.0"
+    micromark-util-symbol: "npm:^2.0.0"
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+  resolution: "oniguruma-to-es@npm:4.3.6"
+  dependencies:
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+    regex-recursion: "npm:^6.0.2"
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+    "@shikijs/themes": "npm:4.3.0"
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-"twoslash@npm:0.2.12, twoslash@npm:^0.2.12":
-  version: 0.2.12
-  resolution: "twoslash@npm:0.2.12"
+"twoslash-vue@npm:^0.3.9":
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-    twoslash-protocol: "npm:0.2.12"
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