diff --git a/pkgs/by-name/ja/jabref/deps.json b/pkgs/by-name/ja/jabref/deps.json
index cf671cd8725e..806de87d2389 100644
--- a/pkgs/by-name/ja/jabref/deps.json
+++ b/pkgs/by-name/ja/jabref/deps.json
@@ -652,13 +652,13 @@
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    "pom": "sha256-rECp8tDB7mMfw7CO+OLwvRS6IgEcp2/xvPZftWnq3zU="
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-   "module": "sha256-QfjCNSMXc2dWDubRXMC9a8GqRP6x2BjXihzt2+IMC40=",
-   "pom": "sha256-G9F/hR9bve0OCz16YZzBdxKrmEXqpFu8ypBxX86jEF8="
+  "org/gradle/kotlin#gradle-kotlin-dsl-plugins/6.4.2": {
+   "jar": "sha256-MwhkX0Z7Jm5YhMJkUIIktnKejtwWbm1DX1tibBTg/Rk=",
+   "module": "sha256-kxqze7wDwJHt/8RtlqYLXk+isLTV2UWLkscm4FpR0NM=",
+   "pom": "sha256-VGkK7nfKVycLvqXnhrnTPiOvYIzuIVuIDvcq45v5aU8="
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-  "org/gradle/kotlin/kotlin-dsl#org.gradle.kotlin.kotlin-dsl.gradle.plugin/6.4.1": {
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+  "org/gradle/kotlin/kotlin-dsl#org.gradle.kotlin.kotlin-dsl.gradle.plugin/6.4.2": {
+   "pom": "sha256-Xi2xvrvUHGTWc1VEsphssmofxmiX0ZCXnJC1C4fIXfo="
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   "org/gradle/toolchains#foojay-resolver/1.0.0": {
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@@ -762,146 +762,146 @@
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-   "pom": "sha256-HOL7NczYP8vJCuXFmN/bsilS0IVHgElEpbIfLEbKwL0="
+  "org/jetbrains/kotlin#abi-tools-api/2.2.21": {
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+   "pom": "sha256-kkkKzKD0UFgdVs4FeWHY/6mDVYfmn2bpbQpxdbrOzYU="
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-  "org/jetbrains/kotlin#fus-statistics-gradle-plugin/2.2.20": {
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-   "pom": "sha256-P6gmRiy9hG0YAgLyLFGTQYy5zan2lcmUEjWpsbXBQdk="
+  "org/jetbrains/kotlin#fus-statistics-gradle-plugin/2.2.21": {
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+   "pom": "sha256-JQzsmn5XTCwRF+7PBCHjIAHqDzSwqQHH+k6tb+jd7aQ="
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-  "org/jetbrains/kotlin#fus-statistics-gradle-plugin/2.2.20/gradle813": {
-   "jar": "sha256-OmlZW2x1+/ktMgFodFxpj/cRS4YHhBBQ1ISYgjAG6HE="
+  "org/jetbrains/kotlin#fus-statistics-gradle-plugin/2.2.21/gradle813": {
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+   "pom": "sha256-Bhpvb0xNvpCtDeOeUeeKuvtmf+jJsJXODA3qM1aPQh8="
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-   "jar": "sha256-MYCcvl5312WyQRFT6huuR2cQQGoXfjmhC/ZKYSOgRfI="
+  "org/jetbrains/kotlin#kotlin-assignment/2.2.21/gradle813": {
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-   "jar": "sha256-+5n/fwzZUtpo1UjT89ZErlB4sLlvybrwZewUZqKTuAU=",
-   "pom": "sha256-iTjGIFKXW7uW3OotqaeNS2sk2vLwnTWMGnqEHxaMtzo="
+  "org/jetbrains/kotlin#kotlin-scripting-common/2.2.21": {
+   "jar": "sha256-QU7ZHD9eRJKyPLlTeEK0ZRA44l2thBB5OfQ0wiA/KpI=",
+   "pom": "sha256-7CWpeZRRdbrSFlRqSEsLj0SoZwVZGV4kCzR/H9oXcN8="
   },
-  "org/jetbrains/kotlin#kotlin-scripting-compiler-embeddable/2.2.20": {
-   "jar": "sha256-2GJhDAAzQuUIjKIcRAQix9ijcA4ZnWA/ehAnjESIR2E=",
-   "pom": "sha256-PW9vFZH6P3r14jFlxowu4BclFYZFQ09eMBdF5kfHVhE="
+  "org/jetbrains/kotlin#kotlin-scripting-compiler-embeddable/2.2.21": {
+   "jar": "sha256-2TS50MJGvAliS3Bor1itV87xHb4q3bx7GdJQzOQt4ck=",
+   "pom": "sha256-EUhmLJXzbgCYEXj7LYldBrLs59BX7YRTLdNTu9bDVlA="
   },
-  "org/jetbrains/kotlin#kotlin-scripting-compiler-impl-embeddable/2.2.20": {
-   "jar": "sha256-e3kSNZL//r81xhag/xBDMscc3mN6ZX4JrbXfbD+cA84=",
-   "pom": "sha256-+l+wJ+4qSbPb/zh3VBtC+3CuzMN7oC4dOthipcZyVLc="
+  "org/jetbrains/kotlin#kotlin-scripting-compiler-impl-embeddable/2.2.21": {
+   "jar": "sha256-eIowYMjnmX+K4WulwCgNBQBa8KQgKfGMsQxWJbl5+sM=",
+   "pom": "sha256-DKT5XDLUrpVOF06kHlutYseNvJOmTEUHb96czISrNgk="
   },
-  "org/jetbrains/kotlin#kotlin-scripting-jvm/2.2.20": {
-   "jar": "sha256-qR+5BJY0oyum09LpGgy5mD4KpOccDC4bKDg4qOBhYx8=",
-   "pom": "sha256-0df8RWSBne6v6OvdcfbyGBf/xVjr0U9HpW6NyTaW3Rk="
+  "org/jetbrains/kotlin#kotlin-scripting-jvm/2.2.21": {
+   "jar": "sha256-g4IMX8xdKPBF+RTs1ZALu8+BFbDXAHM03gaf5scGaeY=",
+   "pom": "sha256-nR1Dsi27irmp3yJ6bVRYNB2v/sFQ73WV12XMXsvxeQg="
   },
   "org/jetbrains/kotlin#kotlin-stdlib-jdk7/1.8.21": {
    "jar": "sha256-M9FI2w4R3r0NkGd9KCQrztkH+cd3MAAP1ZeGcIkDnYY=",
@@ -919,26 +919,26 @@
    "jar": "sha256-FcjArLMRSDwGjRaXUBllR0tw39gKx5WA7KOgPPUeSh0=",
    "pom": "sha256-MQ1tXGVBPjEQuUAr2AdfyuP0vlGdH9kHMTahj+cnvFc="
   },
-  "org/jetbrains/kotlin#kotlin-stdlib/2.2.20": {
-   "jar": "sha256-iDbM/9NYX63amQEkSyDUKQHS881YEFjYQ04v+rzzo+c=",
-   "module": "sha256-yRj1IU0CGnLjdn8nVul9EDpSbgTxQj2jZj79+1hH25U=",
-   "pom": "sha256-SosIbmQxvPYjY39Ssv8ZLhrbkTg4dC5cDupwqN7kKcQ="
+  "org/jetbrains/kotlin#kotlin-stdlib/2.2.21": {
+   "jar": "sha256-ZVij0jPaVqIJNLMhWfnbX4btWBbvCY94osIj3Gq7ed0=",
+   "module": "sha256-v7xlfd06jjfkyK1BeWjV6wsLFxyfzkj5YsKtMu5DTCE=",
+   "pom": "sha256-zzH5IxlsY67ezQpXwkJpvTcCpOR8C/C9ZLWtpd5SInI="
   },
-  "org/jetbrains/kotlin#kotlin-tooling-core/2.2.20": {
+  "org/jetbrains/kotlin#kotlin-tooling-core/2.2.21": {
    "jar": "sha256-dAFOxPPveM59p+Pmlk8sUmoxIdXFj++MopeeXzRFgvQ=",
-   "pom": "sha256-jvep2QYs59w/xlVxXdAoqZRLeElhPgEYR8XWs7mSgXE="
+   "pom": "sha256-3TPmGTLBut893oXyBPY0yABL6WQnw6HKiGbMAR1xHfo="
   },
-  "org/jetbrains/kotlin#kotlin-util-io/2.2.20": {
-   "jar": "sha256-1DGva+puLcmInE/iawc84VfxEchgj+laGL/gi4F8/3Q=",
-   "pom": "sha256-xqXQGEjNBAz8j3uuYjLXktcFwpOi2nJmrmJszbNdagM="
+  "org/jetbrains/kotlin#kotlin-util-io/2.2.21": {
+   "jar": "sha256-JmqkAmoQb1n878PxUXaIcK+RzvFeQBH6wKofH1Z9SfQ=",
+   "pom": "sha256-67UM9Bx0RJdvAsL5FbQXMlcsXzmUplgciOZN4LmY970="
   },
-  "org/jetbrains/kotlin#kotlin-util-klib-metadata/2.2.20": {
-   "jar": "sha256-vuSQHKU6WiHA22RZAdKwcK/2gkAkF91XiODjWTZFcTs=",
-   "pom": "sha256-vtAGUSIGX65328DEb/xBRqaFy7GLijApq9XaO/qhECc="
+  "org/jetbrains/kotlin#kotlin-util-klib-metadata/2.2.21": {
+   "jar": "sha256-AiuVo9/tlJ18LkeCC82YNu4Fe3IVE/dzNh5DM/bHb4w=",
+   "pom": "sha256-87Mj0f6eM9x+nF7XfzBSg//WN4FdiMUHlFQRvXqiow8="
   },
-  "org/jetbrains/kotlin#kotlin-util-klib/2.2.20": {
-   "jar": "sha256-7XyAlrK75HetF8MXjeuoyDr1MourNr/iEJEL1bQZI0w=",
-   "pom": "sha256-2mwiR3qvQt2hbYWa2unj7Yq8khzLp/9RYTTMi9NZqpI="
+  "org/jetbrains/kotlin#kotlin-util-klib/2.2.21": {
+   "jar": "sha256-VUAKkX5rmEphl+rni1tS7b3yzW4KfDhD95VEgbr7JD8=",
+   "pom": "sha256-o1Lf02Uns67w98DsZJDeydX8m+xPM02ETK6U+BdD3zA="
   },
   "org/jetbrains/kotlinx#kotlinx-coroutines-bom/1.8.0": {
    "pom": "sha256-Ejnp2+E5fNWXE0KVayURvDrOe2QYQuQ3KgiNz6i5rVU="
@@ -1203,11 +1203,19 @@
   "com/fasterxml/jackson#jackson-parent/2.20": {
    "pom": "sha256-tDt/XGLoaxZPrnCuF9aRHF22B5mvAQVzYK/aguSEW+U="
   },
+  "com/fasterxml/jackson/core#jackson-annotations/2.17.2": {
+   "module": "sha256-KMxD6Y54gYA+HoKFIeOKt67S+XejbCVR3ReQ9DDz688=",
+   "pom": "sha256-Q3gYTWCK3Nu7BKd4vGRmhj8HpFUqcgREZckQQD+ewLs="
+  },
   "com/fasterxml/jackson/core#jackson-annotations/2.20": {
    "jar": "sha256-lZov+y1ZFDb1Hxg8alIfyJNHkS9xG/DK4AjN8EXZUxk=",
    "module": "sha256-wHDxTsg1jQlcAurootZcsAzLoOXFqnOwASlDM/5GiXE=",
    "pom": "sha256-TXQMRHjdCNCJ7NxtBjIopVoRp+jkl9pDOPhy+BFXlKQ="
   },
+  "com/fasterxml/jackson/core#jackson-core/2.17.2": {
+   "module": "sha256-OCgvt1xzPSOV3TTcC1nsy7Q6p8wxohomFrqqivy38jY=",
+   "pom": "sha256-F4IeGYjoMnB6tHGvGjBvSl7lATTyLY0nF7WNqFnrNbs="
+  },
   "com/fasterxml/jackson/core#jackson-core/2.19.2": {
    "jar": "sha256-qnfq8pKTqGjEc3IZT3xSh9d9k3CwTqJdP//B5JBLWIA=",
    "module": "sha256-Ua8uZ3g6XXJETeajB8jj7ZMAklbNJ+ghkVVZohZcCUI=",
@@ -1897,9 +1905,6 @@
   "net/java/dev/jna#jna/5.13.0": {
    "pom": "sha256-9RXCV4F49FJH7Mp6nh2xCVMbHELyQk4lPO6w9rjUI3Q="
   },
-  "net/java/dev/jna#jna/5.17.0": {
-   "pom": "sha256-UBoP8F2EpK0Q9t4lvpT0k5i3CjG+jzoO2fTGtE++/uQ="
-  },
   "net/java/dev/jna#jna/5.18.1": {
    "jar": "sha256-JgxLHiKx254RDuRBxPE84RX4QfpIxB14dQmGIUs5VVc=",
    "pom": "sha256-mLYq5v8oDXR/s1n8QuSP7RE9Rbw3Kagj3DC4MIqAZkU="
diff --git a/pkgs/by-name/ja/jabref/package.nix b/pkgs/by-name/ja/jabref/package.nix
index 2e31f41c8b30..0a38413359f9 100644
--- a/pkgs/by-name/ja/jabref/package.nix
+++ b/pkgs/by-name/ja/jabref/package.nix
@@ -54,6 +54,7 @@ let
     url = ltwaUrl;
     hash = "sha256-jnS8Y9x8eg2L3L3RPnS6INTs19mEtwzfNIjJUw6HtIY=";
   };
+  kotlinDslVersion = "6.4.2";
 in
 stdenv.mkDerivation rec {
   version = "6.0-alpha.4";
@@ -93,6 +94,9 @@ stdenv.mkDerivation rec {
 
     sed -i -e '1a //REPOS file://${mitmCache}/https/repo.maven.apache.org/maven2,file://${mitmCache}/https/plugins.gradle.org/m2' build-support/src/main/java/*.java
 
+    substituteInPlace build-logic/build.gradle.kts \
+      --replace-fail '`kotlin-dsl`' 'id("org.gradle.kotlin.kotlin-dsl") version "${kotlinDslVersion}"'
+
     pushd jablib
 
     # Disable update check