diff --git a/pkgs/by-name/ja/jabref/deps.json b/pkgs/by-name/ja/jabref/deps.json
index 6b510245eb29..60d15e9c54e4 100644
--- a/pkgs/by-name/ja/jabref/deps.json
+++ b/pkgs/by-name/ja/jabref/deps.json
@@ -1,79 +1,491 @@
 {
  "!comment": "This is a nixpkgs Gradle dependency lockfile. For more details, refer to the Gradle section in the nixpkgs manual.",
  "!version": 1,
- "https://jitpack.io/com/github/sialcasa": {
-  "mvvmFX#mvvmfx-parent/f195849ca9": {
+ "https://jitpack.io/com/github": {
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+   "pom": "sha256-wy8tTwK/IzXbLQH9Gwz/teUyhGO0lDZmvqwaH/ijpRs="
+  },
+  "koppor#wiremock-slf4j-shim/main-4c871b2e09-1/SNAPSHOT": {
+   "jar": "sha256-hYimLyaTZemhJDtmEe7bXPgd6NyKqTlEmUNmppuGRMQ=",
+   "module": "sha256-0hRsMRKmvd7NpykFlfy09yR+mB1dRC1BJ9ZXJMHT3mg=",
+   "pom": "sha256-8zEeXekVsvcVpndak1CfKytwdn66tWZ1P/LMn7AghiM="
+  },
+  "koppor#wiremock-slf4j-spi-shim/main-baf2359720-1/SNAPSHOT": {
+   "jar": "sha256-pMFZcWqiV+eoEWvos2DcosgjcISVkIRJd/frIot7wtY=",
+   "module": "sha256-X/cJ7GFDbk5yxaoKRBL+2WNQaou3AtGjdJ3guAZ5e+I=",
+   "pom": "sha256-eN40hwyeJ7TzUBS5QkTROKe8dU47/PKV5MWGKFgV2pM="
+  },
+  "koppor/jbang-gradle-plugin#build/8a85836163": {
+   "jar": "sha256-EV18C7JMsORCV1SsIU0OAN0RGXwNSxVqHvUUagoFibM=",
+   "pom": "sha256-/UAMODCKxj6CvtciTIXCQDvzZlYH4L3iPe+aI2csWMg="
+  },
+  "koppor/wiremock-slf4j-shim/main-SNAPSHOT/maven-metadata": {
+   "xml": {
+    "groupId": "com.github.koppor"
+   }
+  },
+  "koppor/wiremock-slf4j-spi-shim/main-SNAPSHOT/maven-metadata": {
+   "xml": {
+    "groupId": "com.github.koppor"
+   }
+  },
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    "pom": "sha256-5nTE66pGjgRswUpwK3guGpZb5iI4/2kmYy+wtGIsSz0="
   },
-  "mvvmFX#mvvmfx-validation/f195849ca9": {
+  "sialcasa/mvvmFX#mvvmfx-validation/f195849ca9": {
    "jar": "sha256-Q3dcLohYshPQP3jWb0/Wh6IENg4CGn9Tl8tVvRHVhO0=",
    "pom": "sha256-MplYnkdrZQ8ptd0PuUqUcWe6SwKaoM4VdOOV1KMAPvs="
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-   "pom": "sha256-NudbADyHMI49AKmZi2KOYbTzRW/uuPdiYDDJcwEEPhA="
-  },
-  "tobiasdiez/easybind/2.2.1-SNAPSHOT/maven-metadata": {
+ "https://maven-central.storage-download.googleapis.com": {
+  "repos/central/data/com/google/code/gson/gson/maven-metadata": {
    "xml": {
-    "groupId": "com.tobiasdiez",
-    "lastUpdated": "20230117075740"
+    "groupId": "com.google.code.gson",
+    "lastUpdated": "20191004190047",
+    "release": "2.8.6"
+   }
+  }
+ },
+ "https://oss.sonatype.org/content/groups/public/com/google/code": {
+  "gson#gson/2.13.1": {
+   "pom": "sha256-wPZXItdcDljNGDWzBGBG9ga12mmZBBYfjba3j+ubQBo="
+  },
+  "gson/gson/maven-metadata": {
+   "xml": {
+    "groupId": "com.google.code.gson",
+    "lastUpdated": "20250424011321",
+    "release": "2.13.1"
    }
   }
  },
  "https://plugins.gradle.org/m2": {
+  "aopalliance#aopalliance/1.0": {
+   "jar": "sha256-Ct3sZw/tzT8RPFyAkdeDKA0j9146y4QbYanNsHk3agg=",
+   "pom": "sha256-JugjMBV9a4RLZ6gGSUXiBlgedyl3GD4+Mf7GBYqppZs="
+  },
   "com/adarshr#gradle-test-logger-plugin/4.0.0": {
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    "pom": "sha256-ienBpTqmJS2mx9fZscN/t/j8qQuysaNq+Ti8cNni3GE="
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-  "com/adarshr/test-logger#com.adarshr.test-logger.gradle.plugin/4.0.0": {
-   "pom": "sha256-sobTcqzS2uG4vHsg/ouoT49kiXMdiBpB83NqYCCFotc="
+  "com/autonomousapps#antlr/4.13.2.0": {
+   "jar": "sha256-NIkksRa3slEROvUMG/G1fA33yJuPVkBsH/G+LVtGn70=",
+   "module": "sha256-Hf8N8eJnD4AHPfue2wqmT3gApXk0v0GuY3dX/Ug5Pj4=",
+   "pom": "sha256-mdteD5BV3rEh0K7T+9/HuKF6lizDVIK7kpwnCJG+okw="
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-   "pom": "sha256-/jLkdoa/L/1ARpoP52+JmSmawj38yVpzyzDGf/hsKr4="
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+   "module": "sha256-a7FFF9qhCdcqgO9yeOE5+KaIBs6Ee6Ors7HfJ+pdoo4=",
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+  "com/autonomousapps#variant-artifacts/0.3.3": {
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+   "pom": "sha256-lGpocou8619zbQJurZmQJ7Py6qjt0RnEWnJT5qlK24s="
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+   "pom": "sha256-DVrgvsCUlVKcY8yKbBMlOHBoaDKk47IGwTgWUDWuS8U="
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+  "com/fasterxml#oss-parent/55": {
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@@ -81,13 +493,214 @@
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   "org/fusesource#fusesource-pom/1.12": {
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@@ -96,41 +709,354 @@
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@@ -194,24 +1207,19 @@
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@@ -219,146 +1227,119 @@
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-   "pom": "sha256-8HHKdfDnP5fCS/rKO+385yPOEa2FEk3I0eGDBv7T0qQ="
+  "com/github/ben-manes/caffeine#caffeine/3.0.5": {
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@@ -378,6 +1359,30 @@
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    "pom": "sha256-/wQyxT//a1/dcnAG08orA7lEUjl7g4+PFUby92u0OSM="
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@@ -390,53 +1395,130 @@
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@@ -446,48 +1528,51 @@
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@@ -495,112 +1580,70 @@
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-   "pom": "sha256-GA8sOPoquiEKfyUHxdC1B1FghhfbFK/mvS8iqm/lDbU="
+  "com/uber/nullaway#nullaway/0.12.10": {
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+   "module": "sha256-xhqvAaX6KnYzQnV7MSabFph+weQ5Pv9TGJX/nQkaSDY=",
+   "pom": "sha256-W/XkwpCd2bMZMm0GROWORJ86wSxJwDCuyfswRdw5QB8="
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   "com/vladsch/flexmark#flexmark-ext-emoji/0.64.8": {
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@@ -693,21 +1736,13 @@
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    "pom": "sha256-w1zKe2HUZ42VeMvAuQG4cXtTmr+SVEQdp4uP5g3gZNA="
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-   "pom": "sha256-x3AmC5U07xOUD6CHpbAZasVKZNDc1IXermbErapsF1g="
+  "commons-codec#commons-codec/1.17.1": {
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+   "pom": "sha256-f6DbTYFQ2vkylYuK6onuJKu00Y4jFqXeU1J4/BMVEqA="
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-   "pom": "sha256-bLWVeBnfOTlW/TEaOgw/XuwevEm6Wy0J8/ROYWf6PnQ="
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-   "pom": "sha256-uCbd2S+dfMZDcaAvoIMMFU1nyYNw6lSi0ZbnLrWQrSg="
+  "commons-codec#commons-codec/1.18.0": {
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+   "pom": "sha256-dLkW2ksDhMYZ5t1MGN7+iqQ4f3lSBSU8+0u7L0WM3c4="
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@@ -717,17 +1752,20 @@
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    "pom": "sha256-FaWcDnV8bAfD0baJ1zXI46nsVpXWzrapQdQGKrIpAbc="
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-   "pom": "sha256-Fxoa+CtnWetXQLO4gJrKgBE96vEVMDby9ERZAd/T+R0="
+  "commons-fileupload#commons-fileupload/1.5": {
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-   "pom": "sha256-yRq1qlcNhvb9B8wVjsa8LFAIBAKXLukXn+JBAHOfuyA="
+  "commons-io#commons-io/2.20.0": {
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+   "pom": "sha256-vb34EHLBkO6aixgaXFj1vZF6dQ+xOiVt679T9dvTOio="
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-   "pom": "sha256-UztBf2dHU/bHn6v7/vlqRj6pw8yj16g/8Ot9dmgpP8k="
+  "commons-logging#commons-logging/1.3.5": {
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+   "pom": "sha256-zPSjA0b1AnuUlqvVYpCsJtFZq/K+ZN8SZWEdyUALnWg="
+  },
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+   "pom": "sha256-rQh4fwxzi1BNdoDgb6acXRp0uWPbmADEjl8jJMH13h8="
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   "de/rototor/jeuclid#jeuclid-core/3.1.11": {
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@@ -747,10 +1785,6 @@
   "de/rototor/snuggletex#snuggletex/1.3.0": {
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@@ -762,17 +1796,45 @@
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    "pom": "sha256-29pS9ELRHsCI5GAHXeBCgn0JEB93W8IoQoAZAtM3z+Y="
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-   "pom": "sha256-0LpxAQH7jCteBQxlLPYr+KmZT+6PBv+jzi2BLdkABMk="
+  "de/undercouch#citeproc-java/3.3.0": {
+   "jar": "sha256-cs8SB8VkOg4pLqszz67FfdnWULIpnZEXHcxH0WHkdpY=",
+   "module": "sha256-zagYll9YHJ1KSMexajIOPyQ6UzgHkkEdtKpDAdqT1ZM=",
+   "pom": "sha256-mk/t77P98TXzy9G6mEzVI7FwPy+eF2XEgPwbg10J7/0="
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+  "dev/langchain4j#langchain4j-bom/1.7.1": {
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+  },
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+   "pom": "sha256-pPxwClyaqg8dmfKFx0jKbmMtRcDvD4Sx9HGL0/QHcfY="
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+   "pom": "sha256-f6k1C/GAIH9AwPMqjbxrYlrLNNfLh6kyvg5xgNrmNic="
+  },
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+   "pom": "sha256-QyFCoVzKhQxg4KWKj/sJM7JIMwFXUPih9I+sdkHIi20="
+  },
+  "dev/langchain4j#langchain4j-mistral-ai/1.7.1": {
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+   "pom": "sha256-Uo6pcNepIoKlmRvhV4Qo+GUWT7yT3A/60Lh3N0oIfY4="
+  },
+  "dev/langchain4j#langchain4j-open-ai/1.7.1": {
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+   "pom": "sha256-4htkUZr95BDGH72AMl3rzFNjtDBHsocqpu/KMnxhmzE="
+  },
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+   "pom": "sha256-CroqqYgDZHNjDKydjt16DMastlFJKNWsDFR/Al+KChk="
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@@ -782,53 +1844,102 @@
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    "pom": "sha256-dgQpbIuuApGPJvekSKGwnzjluw2W1XhuTi3yF2B+9No="
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-   "pom": "sha256-fk6LD0t8pgdSCyDS8eWN9Pk0ymNsseuoKJz/LylWv9g="
+  "info/picocli#picocli-codegen/4.7.7": {
+   "jar": "sha256-ba5oIyzh0VK45HTVvRiI0QC8jOoquTB6TlqgThNX0mE=",
+   "pom": "sha256-JsgAo/b7dn4wCrLbF6qhz1NsuEYpo9R1bVQLnB0BwSw="
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+  "info/picocli#picocli/4.7.7": {
+   "jar": "sha256-+G4w//0Q0rE7jKqNSyN6fuYfL/zPWxlB3nGLdl0jW/g=",
+   "pom": "sha256-GxjTYxNN9mYx0rn3R1Bo1zQiW6OJzfkIKhvYvakNV9M="
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-   "pom": "sha256-98UQqlWYvLu+nMT8dqy/mnD0Z3rQkaJy46weuS31zvw="
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@@ -841,86 +1952,94 @@
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@@ -930,19 +2049,25 @@
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-   "pom": "sha256-amd2O3avzZyAuV5cXiR4LRjMGw49m0VK0/h1THa3aBU="
+  "net/minidev#accessors-smart/2.5.0": {
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-  "net/sf/saxon#Saxon-HE/12.4": {
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-   "pom": "sha256-op6LTcFteBhLSANZRkoazPbahWpP31vyugKtTistHBs="
+  "net/minidev#json-smart/2.5.0": {
+   "pom": "sha256-wyo2YQmypaNuoA4SGqolfa5W7jqbl9JEI+YzteIUVGY="
+  },
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@@ -958,23 +2083,16 @@
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@@ -985,48 +2103,46 @@
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+  "org/apache#apache/32": {
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@@ -1035,214 +2151,154 @@
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-   "pom": "sha256-Z8XrD/f1JeoaGY8C2v7nfg0qUxudkIBxvEBhOGrgQO8="
+  "org/eclipse/angus#angus-activation/2.0.3": {
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+   "pom": "sha256-NcnhYgmychJhNU6K6pcWJmSK2dQgHSIb2WkB2QA3LaA="
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@@ -1333,29 +2363,106 @@
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+  "org/eclipse/jetty#jetty-alpn-java-client/11.0.24": {
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-   "pom": "sha256-R9OA2YVT2vdCc5tRC/3ElIp0GHftyypTlvwpGZaJzgk="
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+   "pom": "sha256-kY8QW1fA842FplkTLD77OwSisFUyjtkroXthhDxxvNI="
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+   "pom": "sha256-+hS27PYD01Wuq5hDH+dMq5hGBwPhif48ks7U9pSfnWQ="
+  },
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+   "pom": "sha256-QVoIzIJRwx11jcbNLJ16kLoWWbC+3l0meVVpe6MBtyo="
+  },
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+   "module": "sha256-R0PuegFqASpt8zzShzaiKv7nhN6qOoO5X8YWqNg+VBw=",
+   "pom": "sha256-b3He3vgo4AGrCr+l2+15Adgd9Uzo58ea0kQ8fqkZR0E="
+  },
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+   "module": "sha256-+KGPzb69jD/3+NUqg7/TE/H0LZRl33kDUKQgfIx7tWc=",
+   "pom": "sha256-jVYX1QxejiqosXXT8HDenZxOWn7jgJkSI9dJVyE5p60="
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@@ -1365,293 +2472,230 @@
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    "pom": "sha256-RxdpNVcNIb1oX5VaJavPbwFwmrtaN3Wsj6iVA3fKSZ0="
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-   "pom": "sha256-yoJ5IPQ10QCcug70IeWcw5F0GoYJ/vV0nTZgG/D2k7Q="
+  "org/glassfish/grizzly#grizzly-bom/4.0.2": {
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-   "pom": "sha256-gAUSdml5uc61hhNSs3ZhZDJ/HNSPc2skbJX/x3U+Eo0="
+  "org/glassfish/grizzly#grizzly-framework/4.0.2": {
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+   "pom": "sha256-6t9D2crgPzQMavmLc9fEerafd+k9OP2W1toEr3MnwoM="
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-   "pom": "sha256-RjjOCZYGJo+Joi0e4qgp3FOg/Z9NtiYBjca5EKDSO+k="
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+   "pom": "sha256-5o1kXUXO91e5efhO+z/BMupcwMrGjITyoLu7E2SDfQk="
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-   "pom": "sha256-m6yXc7fb67qrxiRBjoloRX5SEdwBTGbhjMsN4y7+P0Y="
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-   "pom": "sha256-im5GDu34zHuF0zx1YhPmpfeHX0qDg9U10ZnzIR7CNVw="
+  "org/ow2/asm#asm/9.8": {
+   "pom": "sha256-wTZ8O7OD12Gef3l+ON91E4hfLu8ErntZCPaCImV7W6o="
   },
-  "org/ow2/asm#asm-tree/9.5": {
-   "jar": "sha256-PDOmSBkQea6urrfBmkmxU5UvnkD+hvusUgVVTd2azZQ=",
-   "pom": "sha256-pyqq+N0FGJn6CJ54PsfUgnrE19GHYgHG3uy6qUoNyVY="
+  "org/pcollections#pcollections/4.0.1": {
+   "jar": "sha256-H4J2bXwyIZMIVAM76/9Qc+pGtD8nMmB0u+FdFIwYv7M=",
+   "module": "sha256-nr2nwMnbETTTQd/3yK0LxZUyhvvwuZiuyil6HuboCfA=",
+   "pom": "sha256-+j8pi1AlO5bpz7BvARw7zHj9m0DY3NJZCbygRUlzjHE="
   },
-  "org/ow2/asm#asm-tree/9.6": {
-   "jar": "sha256-xD7PF7U5x3fhXae1uGVTs3fi05poPeYoVWfVKDiI5+8=",
-   "pom": "sha256-G8tIHX/Ba5VbtgygfIz6JCS87ni9xAW7oxx9b13C0RM="
-  },
-  "org/ow2/asm#asm-util/9.6": {
-   "jar": "sha256-xjWnQC9Kqb9msvQjDOpiAloP4c1j6HKa3vybGZT6xMM=",
-   "pom": "sha256-UsXB01dAR3nRqZtJqFv506CFAluFFstz2+93yK40AF4="
-  },
-  "org/ow2/asm#asm/9.0": {
-   "jar": "sha256-Dfl1dJFK7pL9NJ0MtOAPM0XUWywjngu1DwqQ6tR4iOA=",
-   "module": "sha256-ivgQlu06/6OaRyn8kApVtmOJSRHWfE1L7w6kJDk90/k=",
-   "pom": "sha256-3gNVWQ3Rv8zNyNeQJK6ZKXLoVSaKztua1oLQheA6lK0="
-  },
-  "org/ow2/asm#asm/9.5": {
-   "jar": "sha256-ti6EtZgHKXUbBFjFNM8TZvcnVCu40VhiEzVoKkYPA1M=",
-   "pom": "sha256-LJzOuVHMZYbejZoWxnKtPkwwucMjAo16PDNmVg1WJ7E="
-  },
-  "org/ow2/asm#asm/9.6": {
-   "jar": "sha256-PG+sJCTbPUqFO2afTj0dnDxVIjXhmjGWc/iHCDwjA6E=",
-   "pom": "sha256-ku7iS8PIQ+SIHUbB3WUFRx7jFC+s+0ZrQoz+paVsa2A="
-  },
-  "org/postgresql#postgresql/42.7.3": {
-   "jar": "sha256-omRMv7obqhRf9+jI71gqbu16fsTKeS9/BUEivex1Ymg=",
-   "pom": "sha256-wqy2hFfZlqjkntB3flklW3RlCXZSOVHxAa25QHXhWIU="
+  "org/postgresql#postgresql/42.7.7": {
+   "jar": "sha256-FXlj1grmbWB+CUZujAzfgIfpyyDQFZiZ/8qWvKJShGA=",
+   "pom": "sha256-qCA7TCFN12Zi0VIdwZaeUYszcJ8IL9nNgTjP9MNpQMw="
   },
   "org/reactfx#reactfx/2.0-M5": {
    "jar": "sha256-ux/CCc2cBXsXpIAz03lPk3unpWazwIstuIh3cnaf3Wc=",
    "pom": "sha256-FdCXejrnQDKd3KigR9gDgnVo5WO+1MLABshBr3/mftE="
   },
-  "org/reflections#reflections/0.10.2": {
-   "jar": "sha256-k4otCP5UBQ12ELlE2N3DoJNVcQ2ea+CqyDjbwE6aKCU=",
-   "pom": "sha256-tsqj6301vXVu1usKKoGGi408D29CJE/q5BdgrGYwbYc="
-  },
-  "org/rnorth/duct-tape#duct-tape/1.0.8": {
-   "jar": "sha256-Mc7xLd7JedH4bXz3CMQaF9pSPQXGhf1mQunQsq3bckA=",
-   "pom": "sha256-Jjb2bevm4SQ3Yy8jpnubyWGwNjMAnlJSeju8hx9AabQ="
-  },
   "org/scala-lang#scala-library/2.13.8": {
    "jar": "sha256-oIgrglFBkMK6x9GkWYcqdfAF/A8+iLK8A5A2cUbjXbc=",
    "pom": "sha256-SucLPLDCFdaa6sKMkhLmgR+euXiVZ4I0BgiTNCCIDVI="
   },
-  "org/slf4j#jul-to-slf4j/2.0.12": {
-   "jar": "sha256-hPAoZMq4Zv+xlu0gIrG42mgupvs9ShYQaUKeg5HuKXk=",
-   "pom": "sha256-cSxGGjt/ZQhXk27ruv6k8afSqsHlVheuJM4+vjkorEg="
+  "org/slf4j#jul-to-slf4j/2.0.17": {
+   "jar": "sha256-p6/NI7nP0UdeVclPlDuAjFkiA15+LCpcZaSHpBBrxTg=",
+   "pom": "sha256-OMMwoKtfCT5WK1L7Ya7GMK4cH5FAbjz1R3UEXlzPbAM="
   },
-  "org/slf4j#slf4j-api/1.7.36": {
-   "jar": "sha256-0+9XXj5JeWeNwBvx3M5RAhSTtNEft/G+itmCh3wWocA=",
-   "pom": "sha256-+wRqnCKUN5KLsRwtJ8i113PriiXmDL0lPZhSEN7cJoQ="
+  "org/slf4j#slf4j-api/2.0.17": {
+   "jar": "sha256-e3UdlSBhlU1av+1xgcH2RdM2CRtnmJFZHWMynGIuuDI=",
+   "pom": "sha256-FQxAKH987NwhuTgMqsmOkoxPM8Aj22s0jfHFrJdwJr8="
   },
-  "org/slf4j#slf4j-api/2.0.12": {
-   "jar": "sha256-p5UCuKvfvXIoRqJ2kSJqQIhoLW01ZU+bgOKpzKz37Uc=",
-   "pom": "sha256-Udh5pZmPWCJ0Dc9VIsDtaXGtXEpeowtw9bVGCT5rQmM="
+  "org/slf4j#slf4j-bom/2.0.17": {
+   "pom": "sha256-940ntkK0uIbrg5/BArXNn+fzDzdZn/5oGFvk4WCQMek="
   },
-  "org/slf4j#slf4j-bom/2.0.12": {
-   "pom": "sha256-SH70mE1wFY9Yw3zodmkxukx+VzdYZYhLdWORv9bQDDk="
-  },
-  "org/slf4j#slf4j-parent/1.7.36": {
-   "pom": "sha256-uziNN/vN083mTDzt4hg4aTIY3EUfBAQMXfNgp47X6BI="
-  },
-  "org/slf4j#slf4j-parent/2.0.12": {
-   "pom": "sha256-fGvEdX5NSZJN3w/sX1zkAvg6bGzz4QUtGVsSgqeFVd4="
+  "org/slf4j#slf4j-parent/2.0.17": {
+   "pom": "sha256-lc1x6FLf2ykSbli3uTnVfsKy5gJDkYUuC1Rd7ggrvzs="
   },
   "org/sonatype/oss#oss-parent/5": {
    "pom": "sha256-FnjUEgpYXYpjATGu7ExSTZKDmFg7fqthbufVqH9SDT0="
@@ -2055,21 +2994,18 @@
   "org/sonatype/oss#oss-parent/9": {
    "pom": "sha256-+0AmX5glSCEv+C42LllzKyGH7G8NgBgohcFO8fmCgno="
   },
-  "org/springframework#spring-framework-bom/5.3.32": {
-   "module": "sha256-R6cJH2l8pjEYXtQY8Morhu7wyCqhbRdx3exLLDu3s70=",
-   "pom": "sha256-glr3ES49kupDa7DfeMGVFIhfXAFtD8YMiyTUdjoBWhA="
+  "org/springframework#spring-framework-bom/5.3.39": {
+   "module": "sha256-+ItA4qUDM7QLQvGB7uJyt17HXdhmbLFFvZCxW5fhg+M=",
+   "pom": "sha256-9tSBCT51dny6Gsfh2zj49pLL4+OHRGkzcada6yHGFIs="
   },
-  "org/testcontainers#testcontainers/1.19.7": {
-   "jar": "sha256-xjfgJnjOvRKjAZqw/QWu9actBCkfC3OPGASZciMSgGw=",
-   "pom": "sha256-cKoV/o9xafOk76fPgfcIpIHMucsuCUe2Qh9ZKwjTDkU="
+  "org/testcontainers#testcontainers-bom/1.20.1": {
+   "pom": "sha256-CKrS6R3QXKeycG0t/Ap66AxLXFBHAweZyLzbcyfLL0A="
   },
-  "org/testfx#testfx-core/4.0.16-alpha": {
-   "jar": "sha256-d0OENQCPIFYHClNrpQE9YxtPjBJv/1tTpJgh0Ml6dVE=",
-   "pom": "sha256-WgPqJdnH2bzqrnSheRJYPpZEpfUPENk20ovgMHzuyhs="
+  "org/testfx#testfx-core/4.0.18": {
+   "pom": "sha256-+rVBhIAbFZm8WzBb8R0X3ACeT1lqUXwT3BxUb6jdOxo="
   },
-  "org/testfx#testfx-junit5/4.0.16-alpha": {
-   "jar": "sha256-QFZZthIlFxY+GwQdr3WL6q7Y2PQKmtRXEkhiUTrSbZI=",
-   "pom": "sha256-US6tI6KaaXRc4VgL44P/L1XE+2ts0tAoOjJCOo1sQcQ="
+  "org/testfx#testfx-junit5/4.0.18": {
+   "pom": "sha256-tf7EtIJi2i0sWif2B0C/H9b1ChVVy45wtRgNr55fZLA="
   },
   "org/tinylog#slf4j-tinylog/2.7.0": {
    "jar": "sha256-UdOqc6mGv8mFPuqRzXGHe5eJHwHIX2m0Kie1u5YpXeI=",
@@ -2083,61 +3019,57 @@
    "jar": "sha256-N+Uy9wagG7dqmEVMzXHR/6LoPyvv4cMJ5cZ+PEdL7bo=",
    "pom": "sha256-mfmyIjpFEnD+OiS3DkfSXS46HWyYW0AxzReI/l1jt8Q="
   },
-  "org/xerial/snappy#snappy-java/1.1.10.5": {
-   "jar": "sha256-Dz8YV+0zEWWD9IC031wCGINsR7+8nGIhwNc/NW3s83s=",
-   "pom": "sha256-ZfW4PkjZ5JRIKtA/GEyeV680jXj0rr4AzWr9xnaB7Y0="
+  "org/tukaani#xz/1.10": {
+   "jar": "sha256-lcY8GlWyLdZFOJCkGcwaZA95C799iugtseMK7++wiIg=",
+   "pom": "sha256-72CLg8O7bI4+azvqo4hCuhWWO0ZJXkr5GwdGyLdQ87k="
   },
-  "org/xmlresolver#xmlresolver/5.2.2": {
-   "jar": "sha256-78kr1+0ys+VwleCz6HIFHM+73MmAgx7zPonjgWGoUiI=",
-   "module": "sha256-GwTrOc/sj9X44KtqVSGymabUTza3o8Vx+6lr5Tp26AU=",
-   "pom": "sha256-4VopIlQ7OlXDF3TxDoPbdOk7L6kLPWMV3TocQqkfAHQ="
+  "org/wiremock#wiremock/3.13.0": {
+   "module": "sha256-6UqHsje9650nqsFtS6+ujcPjsXblK3tBQSOKrhEsZgs=",
+   "pom": "sha256-8DaGoIr4nd2qb8RQ2/havBO4oKS99AXlSZo2vLhLjZ4="
   },
-  "org/xmlresolver#xmlresolver/5.2.2/data": {
-   "jar": "sha256-FzkEvb14O6D6ySxbzAXaXQnwzn7tJDRmZuoKI5Rh+bQ="
+  "org/xmlunit#xmlunit-core/2.10.4": {
+   "pom": "sha256-QMVRcQPPFS8IejttyqpTDs5h8D1/KUSR/4gtk2utBl8="
   },
-  "org/xmlunit#xmlunit-core/2.9.1": {
-   "jar": "sha256-fnDyPU914F8O558Pa54Tts9R0082xfw6a4OUKd3h7+8=",
-   "pom": "sha256-0n5OKjEqIVR+82BcgS5+YMiuyWTn+WDlDU3Dy2azkBI="
+  "org/xmlunit#xmlunit-legacy/2.10.0": {
+   "pom": "sha256-B0sBekWQP79QoP3faxekM90lzFQDmMGvuG+tkOxxwmg="
   },
-  "org/xmlunit#xmlunit-matchers/2.9.1": {
-   "jar": "sha256-uAyzm0wip1yGgQbGJoG/K64aWB9D82s1x74qz52d1GY=",
-   "pom": "sha256-EuxNwYrSDy5ojDCKgHWYl4ZE8T2bsTrqkDKlUEvQIK0="
+  "org/xmlunit#xmlunit-matchers/2.10.4": {
+   "pom": "sha256-JH4kA3uLcvdMy7TUXzVPlJ1VUQTeyL7U6K/dVleCvww="
   },
-  "org/xmlunit#xmlunit-parent/2.9.1": {
-   "pom": "sha256-1+RY+9XGRFBIeOX7zglLHTB402mn/uF93ezj0Zn9qsA="
+  "org/xmlunit#xmlunit-parent/2.10.0": {
+   "pom": "sha256-XOnCkW1QdlQJ78IKgQf5jvF3BAzr4LG4VwSI4h0JYcc="
   },
-  "org/yaml#snakeyaml/2.2": {
-   "jar": "sha256-FGeTFEiggXaWrigFt7iyC/sIJlK/nE767VKJMNxJOJs=",
-   "pom": "sha256-6YLq3HiMac8uTeUKn2MrGCwx26UGEoMNNI/EtLqN19Y="
+  "org/xmlunit#xmlunit-parent/2.10.4": {
+   "pom": "sha256-g9gzkrJTxbwHpRKgjYt5RiPn1MW7u6DE25H0zjeAkeI="
+  },
+  "org/xmlunit#xmlunit-placeholders/2.10.0": {
+   "pom": "sha256-41+qK1zuBc03FaViqCOoA4/PQyp97WWZny0lBaGMSes="
+  },
+  "org/yaml#snakeyaml/2.5": {
+   "jar": "sha256-5mgqzxrOd1CO8TZJy/T40J0s9UV722HSX/tqwCM9eN0=",
+   "pom": "sha256-ugGuenRMtS/o7POwI8vDLgzMjGvu+fJt53pHgII5RH0="
   },
   "pt/davidafsilva/apple#jkeychain/1.1.0": {
    "jar": "sha256-DBAKBPcAbxpuRxOFMF2IORIFaO29gPV7eHtxq415sXM=",
    "module": "sha256-jMj9dmUna3xQ+fSqQtV4t40JKzy8ts0F/TKffE36A40=",
    "pom": "sha256-McjawxJZPkNy5BS90l5/ggozTuwD/itb0p4daocwRKg="
   },
-  "tech/units#indriya/2.1.2": {
-   "jar": "sha256-KGUPPEehW1AM1XkXaZKqWfbcQwqEKQqd7Svhly0r/eA=",
-   "pom": "sha256-ydZchn1fU9Z4XogcMASiwBCmk9EcCT8y03eiwHWxz9c="
+  "tech/units#indriya/2.2.3": {
+   "jar": "sha256-w3NPevPuwgt5npaB27jrTbUTkqqvpr5ksD6JmcDgwQk=",
+   "pom": "sha256-OF6hZbmDyIXO3fX+jGmONo/bMm74r7HvDPD5dMANJNQ="
   },
-  "tech/uom#uom-parent/2.1": {
-   "pom": "sha256-iIrWpNud30ZNQcX1Jf0E95C5yTmoEPEWskVBw6ndFpM="
+  "tech/uom#uom-parent/2.2": {
+   "pom": "sha256-r+BsBrxk+tTcsiqyq2pyyLRnH5abuU90KyRqxP9Vmjo="
   },
-  "tech/uom#uom-parent/2.1.1": {
-   "pom": "sha256-rNe3raemg444OLgoG3V4Hoo+mKSZm79kjwsNiBHXSe0="
+  "tech/uom#uom-parent/2.2.3": {
+   "pom": "sha256-8Mgzb4y2X2bFwVBR2Qp25WMMI1ndQvxV+9IXjAHFRRA="
   },
-  "tech/uom/lib#uom-lib-common/2.1": {
-   "jar": "sha256-YYJfVNYd2pvalSU7QHZTvhz5/ZuUHaNGLJSjsW8rHIg=",
-   "pom": "sha256-ZyShzOK9EVWuZmGJ5j6Hzyu2tScCqxqLZsgY18dufvg="
+  "tech/uom/lib#uom-lib-common/2.2": {
+   "jar": "sha256-oB7OHCNrexWkMbA4O93fBtxteoUpDppitjkE4eTg3A0=",
+   "pom": "sha256-ndT8yLY75Zvu29WHZwLYLUQ5ySpxgU9TrkL0p/SohNA="
   },
-  "tech/uom/lib#uom-lib/2.1": {
-   "pom": "sha256-x71alqfCcTCj8zlti6X9PO7yPTE9k8wAexFAKlJzjbY="
-  }
- },
- "https://sandec.jfrog.io": {
-  "artifactory/repo/one/jpro/jproutils#tree-showing/0.2.2": {
-   "jar": "sha256-UL0OKkyxsS6fmZUT19xz7XRE6xGDirJwOPh/42G7wk0=",
-   "module": "sha256-MIj5KRKf67jwt1J/uusje3MSfHk6PB4wVAPLpTn3xC8=",
-   "pom": "sha256-fP6x7y/1WE9jjIYlE+o+8IyFw0gTyzvHDOPTUyQLTMw="
+  "tech/uom/lib#uom-lib/2.2": {
+   "pom": "sha256-EUCfWa/BJ74iyO5VCUNHZPSB5mX3FMBz5HGciB0oM8k="
   }
  }
 }
diff --git a/pkgs/by-name/ja/jabref/package.nix b/pkgs/by-name/ja/jabref/package.nix
index e35decacd0e8..d8f0363e0390 100644
--- a/pkgs/by-name/ja/jabref/package.nix
+++ b/pkgs/by-name/ja/jabref/package.nix
@@ -1,35 +1,43 @@
 {
   lib,
   stdenv,
+  fetchurl,
   fetchFromGitHub,
   wrapGAppsHook3,
   makeDesktopItem,
   copyDesktopItems,
+  makeShellWrapper,
   unzip,
+  zip,
   xdg-utils,
   gtk3,
-  jdk21,
+  jdk25,
   openjfx25,
-  gradle_8,
+  gradle_9,
   python3,
+  postgresql,
+  jbang,
 }:
+
 let
-  jdk = jdk21.override {
-    enableJavaFX = true;
-    openjfx_jdk = openjfx25;
+  jdk = jdk25;
+  openjfx = openjfx25;
+  gradle = gradle_9;
+  ltwaUrl = "https://www.issn.org/wp-content/uploads/2021/07/ltwa_20210702.csv";
+  ltwa = fetchurl {
+    url = ltwaUrl;
+    hash = "sha256-jnS8Y9x8eg2L3L3RPnS6INTs19mEtwzfNIjJUw6HtIY=";
   };
-  # "Deprecated Gradle features were used in this build, making it incompatible with Gradle 9.0."
-  gradle = gradle_8;
 in
 stdenv.mkDerivation rec {
-  version = "5.13";
+  version = "6.0-alpha.3";
   pname = "jabref";
 
   src = fetchFromGitHub {
     owner = "JabRef";
     repo = "jabref";
-    rev = "v${version}";
-    hash = "sha256-inE2FXAaEEiq7343KwtjEiTEHLtn01AzP0foTpsLoAw=";
+    tag = "v${version}";
+    hash = "sha256-ZX4LQe8xKZCDJqVh+L9BHkJK82Pz/qPhlaE8SrAin6o=";
     fetchSubmodules = true;
   };
 
@@ -38,7 +46,7 @@ stdenv.mkDerivation rec {
       comment = meta.description;
       name = "JabRef";
       desktopName = "JabRef";
-      genericName = "Bibliography manager";
+      genericName = "BibTex Editor";
       categories = [ "Office" ];
       icon = "jabref";
       exec = "JabRef %U";
@@ -53,22 +61,42 @@ stdenv.mkDerivation rec {
   };
 
   postPatch = ''
+    sed -i -e '/vendor/d' -e '/JavaLanguageVersion/s/24/25/' build-logic/src/main/kotlin/org.jabref.gradle.feature.compile.gradle.kts
+    sed -i -e '/javafx-base/s/24.0.1/25/' build-support/src/main/java/*.java
+
+    substituteInPlace build-support/src/main/java/*.java \
+      --replace-fail 'JAVA 24' 'JAVA 25'
+
+    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
+
+    pushd jablib
+
     # Disable update check
-    substituteInPlace src/main/java/org/jabref/preferences/JabRefPreferences.java \
-      --replace 'VERSION_CHECK_ENABLED, Boolean.TRUE' \
+    substituteInPlace src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java \
+      --replace-fail 'VERSION_CHECK_ENABLED, Boolean.TRUE' \
         'VERSION_CHECK_ENABLED, Boolean.FALSE'
 
     # Find OpenOffice/LibreOffice binary
     substituteInPlace src/main/java/org/jabref/logic/openoffice/OpenOfficePreferences.java \
-      --replace '/usr' '/run/current-system/sw'
+      --replace-fail '/usr' '/run/current-system/sw'
+
+    sed -i -e '/setOutputRedirector/d' src/main/java/org/jabref/logic/search/PostgreServer.java
+
+    substituteInPlace build.gradle.kts \
+      --replace-fail '${ltwaUrl}' 'file://${ltwa}'
+
+    popd
   '';
 
   nativeBuildInputs = [
     jdk
     gradle
+    (jbang.override { inherit jdk; })
     wrapGAppsHook3
     copyDesktopItems
     unzip
+    zip
+    makeShellWrapper
   ];
 
   buildInputs = [
@@ -92,62 +120,96 @@ stdenv.mkDerivation rec {
 
     install -dm755 $out/share/java/jabref
     install -Dm644 LICENSE $out/share/licenses/jabref/LICENSE
-    install -Dm644 src/main/resources/icons/jabref.svg $out/share/pixmaps/jabref.svg
+    install -Dm644 jabgui/src/main/resources/icons/jabref.svg $out/share/pixmaps/jabref.svg
 
     # script to support browser extensions
-    install -Dm755 buildres/linux/jabrefHost.py $out/lib/jabrefHost.py
+    install -Dm755 jabgui/buildres/linux/jabrefHost.py $out/lib/jabrefHost.py
     patchShebangs $out/lib/jabrefHost.py
-    install -Dm644 buildres/linux/native-messaging-host/firefox/org.jabref.jabref.json $out/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json
+    install -Dm644 jabgui/buildres/linux/native-messaging-host/firefox/org.jabref.jabref.json $out/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json
     sed -i -e "s|/opt/jabref|$out|" $out/lib/mozilla/native-messaging-hosts/org.jabref.jabref.json
 
     # Resources in the jar can't be found, workaround copied from AUR
-    cp -r build/resources $out/share/java/jabref
+    cp -r */build/resources $out/share/java/jabref
 
-    tar xf build/distributions/JabRef-${version}.tar -C $out --strip-components=1
-
-    DEFAULT_JVM_OPTS=$(sed -n -E "s/^DEFAULT_JVM_OPTS='(.*)'$/\1/p" $out/bin/JabRef | sed -e "s|\$APP_HOME|$out|g" -e 's/"//g')
+    for tarball in */build/distributions/*.tar; do
+      tar xf $tarball -C $out --strip-components=1
+    done
 
     # Temp fix: openjfx doesn't build with webkit
     unzip $out/lib/javafx-web-*-*.jar libjfxwebkit.so -d $out/lib/
 
+    # Use postgresql from nixpkgs since the bundled binary doesn't work on NixOS
+    ARCH1=${if stdenv.isAarch64 then "arm64v8" else "amd64"}
+    ARCH2=${if stdenv.isAarch64 then "arm_64" else "x86_64"}
+    mkdir postgresql
+    cd postgresql
+    ln -s ${postgresql}/{lib,share} ./
+    mkdir -p bin
+    ln -s ${postgresql}/bin/{postgres,initdb} ./bin
+    # Wrap pg_ctl to workaround https://github.com/NixOS/nixpkgs/issues/83770
+    # Use custom wrap to workaround https://github.com/NixOS/nixpkgs/issues/330471
+    makeShellWrapper ${postgresql}/bin/pg_ctl ./bin/pg_ctl \
+      --add-flags '-o "-k /tmp"'
+    chmod +x ./bin/pg_ctl
+
+    jar=$(ls $out/lib/embedded-postgres-binaries-linux-$ARCH1-*.jar)
+
+    tar -cJf postgres-linux-$ARCH2.txz *
+    zip $jar postgres-linux-$ARCH2.txz
+    cd ..
+
     runHook postInstall
   '';
 
   postFixup = ''
-    rm $out/bin/*
+    for bin in jabgui jabkit jabsrv-cli; do
+      DEFAULT_JVM_OPTS=$(sed -n -E "s/^DEFAULT_JVM_OPTS='(.*)'$/\1/p" $out/bin/$bin | sed -e 's/"//g')
+      MODULE_PATH=$(sed -n -E 's/^MODULE_PATH=(.*)$/\1/p' $out/bin/$bin | sed -e "s|\$APP_HOME|$out|g")
+      MODULE=$(sed -n -E 's/\s*--module (.*) \\/\1/p' $out/bin/$bin)
+      rm $out/bin/$bin*
 
-    # put this in postFixup because some gappsWrapperArgs are generated in gappsWrapperArgsHook in preFixup
-    makeWrapper ${jdk}/bin/java $out/bin/JabRef \
-      "''${gappsWrapperArgs[@]}" \
-      --suffix PATH : ${lib.makeBinPath [ xdg-utils ]} \
-      --add-flags "-Djava.library.path=$out/lib/ --patch-module org.jabref=$out/share/java/jabref/resources/main" \
-      --add-flags "$DEFAULT_JVM_OPTS"
+      # put this in postFixup because some gappsWrapperArgs are generated in gappsWrapperArgsHook in preFixup
+      makeWrapper ${jdk}/bin/java $out/bin/$bin \
+        "''${gappsWrapperArgs[@]}" \
+        --suffix PATH : ${
+          lib.makeBinPath [
+            xdg-utils
+            postgresql
+          ]
+        } \
+        --add-flags "$DEFAULT_JVM_OPTS \
+          -Djava.library.path=$out/lib/:${openjfx}/modules_libs/javafx.graphics:${openjfx}/modules_libs/javafx.media \
+          --module-path $MODULE_PATH \
+          --module $MODULE"
+    done
 
     # lowercase alias (for convenience and required for browser extensions)
-    ln -sf $out/bin/JabRef $out/bin/jabref
+    ln -sf $out/bin/jabgui $out/bin/jabref
+    ln -sf $out/bin/jabgui $out/bin/JabRef
   '';
 
   gradleUpdateScript = ''
-    runHook preBuild
+    # Add jbang deps to gradle
+    sed -n 's|//DEPS \(.*\)|    implementation("\1")|p' build-support/src/main/java/*.java | sort -u | sed -i '/dependencies {/r /dev/stdin' build-logic/build.gradle.kts
 
-    gradle nixDownloadDeps -Dos.arch=amd64
-    gradle nixDownloadDeps -Dos.arch=aarch64
+    gradle assemble -Dos.arch=amd64
+    gradle assemble -Dos.arch=aarch64
   '';
 
-  meta = with lib; {
+  meta = {
     description = "Open source bibliography reference manager";
     homepage = "https://www.jabref.org";
-    sourceProvenance = with sourceTypes; [
+    sourceProvenance = with lib.sourceTypes; [
       fromSource
       binaryBytecode # source bundles dependencies as jars
       binaryNativeCode # source bundles dependencies as jars
     ];
-    license = licenses.mit;
+    license = lib.licenses.mit;
     platforms = [
       "x86_64-linux"
       "aarch64-linux"
     ];
-    maintainers = with maintainers; [
+    maintainers = with lib.maintainers; [
       linsui
     ];
   };