diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix
index 80d272221f31..8b22273ebd87 100644
--- a/maintainers/maintainer-list.nix
+++ b/maintainers/maintainer-list.nix
@@ -11785,12 +11785,6 @@
     githubId = 4599384;
     name = "Jack Baldry";
   };
-  jdehaas = {
-    email = "qqlq@nullptr.club";
-    github = "jeroendehaas";
-    githubId = 117874;
-    name = "Jeroen de Haas";
-  };
   jdelStrother = {
     email = "me@delstrother.com";
     github = "jdelStrother";
@@ -14409,12 +14403,11 @@
     name = "Leiser Fernández Gallo";
   };
   leixb = {
-    email = "abone9999+nixpkgs@gmail.com";
+    email = "abone9999@gmail.com";
     matrix = "@leix_b:matrix.org";
     github = "Leixb";
     githubId = 17183803;
     name = "Aleix Boné";
-    keys = [ { fingerprint = "63D3 F436 EDE8 7E1F 1292  24AF FC03 5BB2 BB28 E15D"; } ];
   };
   lejonet = {
     email = "daniel@kuehn.se";
diff --git a/nixos/doc/manual/release-notes/rl-2511.section.md b/nixos/doc/manual/release-notes/rl-2511.section.md
index 60e046780cb7..b353e7b58a6d 100644
--- a/nixos/doc/manual/release-notes/rl-2511.section.md
+++ b/nixos/doc/manual/release-notes/rl-2511.section.md
@@ -140,6 +140,8 @@
 
 - Added `nixos-init`, a Rust-based bashless initialization system for systemd initrd. This allows to build NixOS systems without any interpreter. Enable via `system.nixos-init.enable = true;`.
 
+- [nvme-rs](https://github.com/liberodark/nvme-rs), NVMe monitoring [services.nvme-rs](#opt-services.nvme-rs.enable).
+
 ## Backward Incompatibilities {#sec-release-25.11-incompatibilities}
 
 <!-- To avoid merge conflicts, consider adding your item at an arbitrary place in the list instead. -->
diff --git a/nixos/modules/module-list.nix b/nixos/modules/module-list.nix
index 4611e4efb324..043132db23c2 100644
--- a/nixos/modules/module-list.nix
+++ b/nixos/modules/module-list.nix
@@ -1502,6 +1502,7 @@
   ./services/system/localtimed.nix
   ./services/system/nix-daemon.nix
   ./services/system/nscd.nix
+  ./services/system/nvme-rs.nix
   ./services/system/saslauthd.nix
   ./services/system/self-deploy.nix
   ./services/system/swapspace.nix
diff --git a/nixos/modules/services/mail/postfix.nix b/nixos/modules/services/mail/postfix.nix
index e69ddcb30866..2c93754b781b 100644
--- a/nixos/modules/services/mail/postfix.nix
+++ b/nixos/modules/services/mail/postfix.nix
@@ -809,7 +809,7 @@ in
         default = "";
         type = lib.types.lines;
         description = ''
-          Entries for the transport map, cf. man-page {manpage}`transport(8)`.
+          Entries for the transport map, cf. man-page {manpage}`transport(5)`.
         '';
       };
 
diff --git a/nixos/modules/services/monitoring/loki.nix b/nixos/modules/services/monitoring/loki.nix
index b3daf470ad9c..e6a4eb535c04 100644
--- a/nixos/modules/services/monitoring/loki.nix
+++ b/nixos/modules/services/monitoring/loki.nix
@@ -25,7 +25,7 @@ let
 in
 {
   options.services.loki = {
-    enable = mkEnableOption "loki";
+    enable = mkEnableOption "Grafana Loki";
 
     user = mkOption {
       type = types.str;
@@ -49,7 +49,7 @@ in
       type = types.path;
       default = "/var/lib/loki";
       description = ''
-        Specify the directory for Loki.
+        Specify the data directory for Loki.
       '';
     };
 
@@ -58,6 +58,10 @@ in
       default = { };
       description = ''
         Specify the configuration for Loki in Nix.
+
+        See [documentation of Grafana Loki](https://grafana.com/docs/loki/latest/configure/) for all available options.
+
+        Cannot be specified together with {option}`services.loki.configFile`.
       '';
     };
 
@@ -66,6 +70,8 @@ in
       default = null;
       description = ''
         Specify a configuration file that Loki should use.
+
+        Cannot be specified together with {option}`services.loki.configuration`.
       '';
     };
 
diff --git a/nixos/modules/services/system/nvme-rs.nix b/nixos/modules/services/system/nvme-rs.nix
new file mode 100644
index 000000000000..ba02ca3cde17
--- /dev/null
+++ b/nixos/modules/services/system/nvme-rs.nix
@@ -0,0 +1,204 @@
+{
+  config,
+  options,
+  lib,
+  pkgs,
+  ...
+}:
+
+let
+  inherit (lib) types;
+  cfg = config.services.nvme-rs;
+  opt = options.services.nvme-rs;
+  settingsFormat = pkgs.formats.toml { };
+in
+{
+  options.services.nvme-rs = {
+    enable = lib.mkEnableOption "nvme-rs, a monitoring service";
+
+    package = lib.mkPackageOption pkgs "nvme-rs" { };
+
+    settings = lib.mkOption {
+      type = types.submodule {
+        freeformType = settingsFormat.type;
+        options = {
+          check_interval_secs = lib.mkOption {
+            type = types.int;
+            default = 3600;
+            description = "Check interval in seconds";
+            example = 86400;
+          };
+
+          thresholds = lib.mkOption {
+            type = types.submodule {
+              freeformType = settingsFormat.type;
+              options = {
+                temp_warning = lib.mkOption {
+                  type = types.int;
+                  default = 55;
+                  description = "Temperature warning threshold (°C)";
+                };
+
+                temp_critical = lib.mkOption {
+                  type = types.int;
+                  default = 65;
+                  description = "Temperature critical threshold (°C)";
+                };
+
+                wear_warning = lib.mkOption {
+                  type = types.int;
+                  default = 20;
+                  description = "Wear warning threshold (%)";
+                };
+
+                wear_critical = lib.mkOption {
+                  type = types.int;
+                  default = 50;
+                  description = "Wear critical threshold (%)";
+                };
+
+                spare_warning = lib.mkOption {
+                  type = types.int;
+                  default = 50;
+                  description = "Available spare warning threshold (%)";
+                };
+
+                error_threshold = lib.mkOption {
+                  type = types.int;
+                  default = 100;
+                  description = "Error count warning threshold";
+                };
+              };
+            };
+            default = { };
+            description = "Threshold configuration for NVMe monitoring";
+          };
+
+          email = lib.mkOption {
+            type = types.nullOr (
+              types.submodule {
+                freeformType = settingsFormat.type;
+                options = {
+                  smtp_server = lib.mkOption {
+                    type = types.str;
+                    default = "smtp.gmail.com";
+                    description = "SMTP server address";
+                    example = "mail.example.com";
+                  };
+
+                  smtp_port = lib.mkOption {
+                    type = types.port;
+                    default = 587;
+                    description = "SMTP server port";
+                  };
+
+                  smtp_username = lib.mkOption {
+                    type = types.str;
+                    description = "SMTP username";
+                    example = "your-email@gmail.com";
+                  };
+
+                  smtp_password_file = lib.mkOption {
+                    type = types.path;
+                    description = "File containing SMTP password";
+                    example = "/run/secrets/smtp-password";
+                  };
+
+                  from = lib.mkOption {
+                    type = types.str;
+                    description = "Sender email address";
+                    example = "nvme-monitor@example.com";
+                  };
+
+                  to = lib.mkOption {
+                    type = types.str;
+                    description = "Recipient email address";
+                    example = "admin@example.com";
+                  };
+
+                  use_tls = lib.mkOption {
+                    type = types.bool;
+                    default = true;
+                    description = "Use TLS for SMTP connection";
+                  };
+                };
+              }
+            );
+            default = null;
+            description = "Email notification configuration";
+          };
+        };
+      };
+      default = { };
+      description = ''
+        Configuration for nvme-rs in TOML format.
+        See the config.toml example for all available options.
+      '';
+    };
+  };
+
+  config = lib.mkIf cfg.enable {
+    services.nvme-rs.settings = opt.settings.default;
+
+    systemd.services.nvme-rs = {
+      description = "NVMe health monitoring service";
+      after = [ "network.target" ];
+      wantedBy = [ "multi-user.target" ];
+
+      serviceConfig =
+        let
+          settingsWithoutNull =
+            if cfg.settings.email == null then lib.removeAttrs cfg.settings [ "email" ] else cfg.settings;
+          configFile = settingsFormat.generate "nvme-rs.toml" settingsWithoutNull;
+        in
+        {
+          ExecStart = lib.escapeShellArgs [
+            "${lib.getExe cfg.package}"
+            "daemon"
+            "--config"
+            "${configFile}"
+          ];
+
+          DynamicUser = true;
+          SupplementaryGroups = [ "disk" ];
+          CapabilityBoundingSet = [ "CAP_SYS_ADMIN" ];
+          AmbientCapabilities = [ "CAP_SYS_ADMIN" ];
+          LimitCORE = 0;
+          LimitNOFILE = 65535;
+          LockPersonality = true;
+          MemorySwapMax = 0;
+          MemoryZSwapMax = 0;
+          PrivateTmp = true;
+          ProcSubset = "pid";
+          ProtectClock = true;
+          ProtectControlGroups = true;
+          ProtectHome = true;
+          ProtectHostname = true;
+          ProtectKernelLogs = true;
+          ProtectKernelModules = true;
+          ProtectKernelTunables = true;
+          ProtectProc = "invisible";
+          ProtectSystem = "strict";
+          Restart = "on-failure";
+          RestartSec = "10s";
+          RestrictAddressFamilies = [
+            "AF_INET"
+            "AF_INET6"
+            "AF_UNIX"
+          ];
+          RestrictNamespaces = true;
+          RestrictRealtime = true;
+          SystemCallArchitectures = "native";
+          SystemCallFilter = [
+            "@system-service"
+            "@resources"
+            "~@privileged"
+          ];
+          NoNewPrivileges = true;
+          UMask = "0077";
+        };
+    };
+
+    environment.systemPackages = [ cfg.package ];
+  };
+}
diff --git a/nixos/tests/all-tests.nix b/nixos/tests/all-tests.nix
index 41862697485c..26a953ab05c7 100644
--- a/nixos/tests/all-tests.nix
+++ b/nixos/tests/all-tests.nix
@@ -1075,6 +1075,7 @@ in
   ntpd = runTest ./ntpd.nix;
   ntpd-rs = runTest ./ntpd-rs.nix;
   nvidia-container-toolkit = runTest ./nvidia-container-toolkit.nix;
+  nvme-rs = runTest ./nvme-rs.nix;
   nvmetcfg = runTest ./nvmetcfg.nix;
   nyxt = runTest ./nyxt.nix;
   nzbget = runTest ./nzbget.nix;
diff --git a/nixos/tests/evcc.nix b/nixos/tests/evcc.nix
index b9896687c2b6..589c8b55843c 100644
--- a/nixos/tests/evcc.nix
+++ b/nixos/tests/evcc.nix
@@ -57,19 +57,19 @@ in
               type = "custom";
               status = {
                 source = "script";
-                cmd = "/bin/sh -c 'echo charger status A'";
+                cmd = "/bin/sh -c 'echo A'";
               };
               enabled = {
                 source = "script";
-                cmd = "/bin/sh -c 'echo charger enabled state false'";
+                cmd = "/bin/sh -c 'echo false'";
               };
               enable = {
                 source = "script";
-                cmd = "/bin/sh -c 'echo set charger enabled state true'";
+                cmd = "/bin/sh -c 'echo true'";
               };
               maxcurrent = {
                 source = "script";
-                cmd = "/bin/sh -c 'echo set charger max current 7200'";
+                cmd = "/bin/sh -c 'echo 7200'";
               };
             }
           ];
diff --git a/nixos/tests/nvme-rs.nix b/nixos/tests/nvme-rs.nix
new file mode 100644
index 000000000000..8f7337916c65
--- /dev/null
+++ b/nixos/tests/nvme-rs.nix
@@ -0,0 +1,157 @@
+{ lib, pkgs, ... }:
+{
+  name = "nvme-rs";
+
+  meta = {
+    maintainers = with lib.maintainers; [ liberodark ];
+  };
+
+  nodes = {
+    monitor =
+      { config, pkgs, ... }:
+      {
+        virtualisation = {
+          emptyDiskImages = [
+            512
+            512
+          ];
+        };
+
+        environment.systemPackages = with pkgs; [
+          nvme-rs
+          jq
+        ];
+
+        services.nvme-rs = {
+          enable = true;
+          package = pkgs.nvme-rs;
+          settings = {
+            check_interval_secs = 60;
+
+            thresholds = {
+              temp_warning = 50;
+              temp_critical = 60;
+              wear_warning = 15;
+              wear_critical = 40;
+              spare_warning = 60;
+              error_threshold = 100;
+            };
+
+            email = {
+              smtp_server = "mail";
+              smtp_port = 25;
+              smtp_username = "nvme-monitor@example.com";
+              smtp_password_file = "/run/secrets/smtp-password";
+              from = "NVMe Monitor <nvme-monitor@example.com>";
+              to = "admin@example.com";
+              use_tls = false;
+            };
+          };
+        };
+
+        systemd.tmpfiles.rules = [
+          "f /run/secrets/smtp-password 0600 root root - testpassword"
+        ];
+
+        networking.firewall.enable = false;
+      };
+
+    mail =
+      { config, pkgs, ... }:
+      {
+        services.postfix = {
+          enable = true;
+          hostname = "mail";
+          domain = "example.com";
+
+          networks = [ "0.0.0.0/0" ];
+          relayDomains = [ "example.com" ];
+          localRecipients = [ "admin" ];
+
+          settings = {
+            main = {
+              inet_interfaces = "all";
+              inet_protocols = "ipv4";
+              smtpd_recipient_restrictions = "permit_mynetworks";
+              smtpd_relay_restrictions = "permit_mynetworks";
+            };
+          };
+        };
+
+        users.users.admin = {
+          isNormalUser = true;
+          home = "/home/admin";
+        };
+
+        networking.firewall = {
+          allowedTCPPorts = [ 25 ];
+        };
+      };
+
+    client =
+      { config, pkgs, ... }:
+      {
+        virtualisation = {
+          emptyDiskImages = [ 256 ];
+        };
+
+        environment.systemPackages = with pkgs; [
+          nvme-rs
+          jq
+        ];
+
+        environment.etc."nvme-rs/config.toml".text = ''
+          check_interval_secs = 3600
+
+          [thresholds]
+          temp_warning = 55
+          temp_critical = 65
+          wear_warning = 20
+          wear_critical = 50
+          spare_warning = 50
+          error_threshold = 5000
+        '';
+      };
+  };
+
+  testScript =
+    { nodes, ... }:
+    ''
+      import json
+
+      start_all()
+
+      for machine in [monitor, mail, client]:
+          machine.wait_for_unit("multi-user.target")
+
+      mail.wait_for_unit("postfix.service")
+      mail.wait_for_open_port(25)
+
+      client.succeed("nvme-rs check || true")
+      client.succeed("nvme-rs check --config /etc/nvme-rs/config.toml || true")
+
+      output = client.succeed("nvme-rs check --format json || echo '[]'")
+      data = json.loads(output)
+      assert isinstance(data, list), "JSON output should be a list"
+
+      monitor.wait_for_unit("nvme-rs.service")
+      monitor.succeed("systemctl is-active nvme-rs.service")
+
+      config_path = monitor.succeed(
+          "systemctl status nvme-rs | grep -oE '/nix/store[^ ]*nvme-rs.toml' | head -1"
+      ).strip()
+
+      if config_path:
+          monitor.succeed(f"grep 'check_interval_secs = 60' {config_path}")
+          monitor.succeed(f"grep 'temp_warning = 50' {config_path}")
+          monitor.succeed(f"grep 'smtp_server = \"mail\"' {config_path}")
+
+      logs = monitor.succeed("journalctl -u nvme-rs.service -n 20 --no-pager")
+      assert "Starting NVMe monitor daemon" in logs or "Check interval" in logs
+
+      monitor.succeed("test -f /run/secrets/smtp-password")
+
+      monitor.succeed("nc -zv mail 25")
+      monitor.fail("nvme-rs daemon --config /nonexistent.toml 2>&1 | grep -E 'Failed to read'")
+    '';
+}
diff --git a/pkgs/applications/editors/emacs/make-emacs.nix b/pkgs/applications/editors/emacs/make-emacs.nix
index 523210b93b80..f1505d45f4f9 100644
--- a/pkgs/applications/editors/emacs/make-emacs.nix
+++ b/pkgs/applications/editors/emacs/make-emacs.nix
@@ -357,6 +357,9 @@ stdenv.mkDerivation (finalAttrs: {
   ]
   ++ lib.optionals withNS [
     librsvg
+  ]
+  ++ lib.optionals (variant == "macport") [
+    librsvg
   ];
 
   # Emacs needs to find movemail at run time, see info (emacs) Movemail
diff --git a/pkgs/applications/emulators/libretro/cores/dosbox-pure.nix b/pkgs/applications/emulators/libretro/cores/dosbox-pure.nix
index f2e7bf164d74..aa1fffc8daf4 100644
--- a/pkgs/applications/emulators/libretro/cores/dosbox-pure.nix
+++ b/pkgs/applications/emulators/libretro/cores/dosbox-pure.nix
@@ -5,13 +5,13 @@
 }:
 mkLibretroCore {
   core = "dosbox-pure";
-  version = "0-unstable-2025-09-14";
+  version = "0-unstable-2025-09-27";
 
   src = fetchFromGitHub {
     owner = "schellingb";
     repo = "dosbox-pure";
-    rev = "78a2d8b7d1354ca60e3f0e39dae18be7c902ece9";
-    hash = "sha256-iNcjB7C833X6jNx0AKv2fJvULke+OCzIc0/3g0SiQwU=";
+    rev = "92d9fbb8111bbb9e8be491315f0e50075036cf0b";
+    hash = "sha256-9MAche3fVHXiUQzhspHTConwkyJCAuRIRaWfEmo8Fko=";
   };
 
   hardeningDisable = [ "format" ];
diff --git a/pkgs/applications/emulators/libretro/cores/gambatte.nix b/pkgs/applications/emulators/libretro/cores/gambatte.nix
index bb9be68937e3..70c202e6b30a 100644
--- a/pkgs/applications/emulators/libretro/cores/gambatte.nix
+++ b/pkgs/applications/emulators/libretro/cores/gambatte.nix
@@ -5,13 +5,13 @@
 }:
 mkLibretroCore {
   core = "gambatte";
-  version = "0-unstable-2025-07-25";
+  version = "0-unstable-2025-09-18";
 
   src = fetchFromGitHub {
     owner = "libretro";
     repo = "gambatte-libretro";
-    rev = "13b7af780e9893ae62cc24d567591b5eb6a6dd72";
-    hash = "sha256-bTNZrXp+kMIq/tnPs73tpYRxlrZfCGCmE0EUlJFtUnY=";
+    rev = "0092232a0aaef0ded0ead1c2003ccf7a85ccdfc0";
+    hash = "sha256-baiTlYArNSBz79Cm16Sg3VZEp909zMkF/ExqhrPYN80=";
   };
 
   meta = {
diff --git a/pkgs/applications/emulators/mame/default.nix b/pkgs/applications/emulators/mame/default.nix
index d2645f8513bc..ff83cad24c3f 100644
--- a/pkgs/applications/emulators/mame/default.nix
+++ b/pkgs/applications/emulators/mame/default.nix
@@ -37,14 +37,14 @@
 
 stdenv.mkDerivation rec {
   pname = "mame";
-  version = "0.280";
+  version = "0.281";
   srcVersion = builtins.replaceStrings [ "." ] [ "" ] version;
 
   src = fetchFromGitHub {
     owner = "mamedev";
     repo = "mame";
     rev = "mame${srcVersion}";
-    hash = "sha256-+bXohqzecHvXt9DKPbBBQoq9RX/LPX0O6kJf64wIrW8=";
+    hash = "sha256-GWb6yu62WDoHz9mWhwjtDUN06r22pXit8pXYhFp/LBw=";
   };
 
   outputs = [
diff --git a/pkgs/development/compilers/adoptopenjdk-icedtea-web/default.nix b/pkgs/by-name/ad/adoptopenjdk-icedtea-web/package.nix
similarity index 98%
rename from pkgs/development/compilers/adoptopenjdk-icedtea-web/default.nix
rename to pkgs/by-name/ad/adoptopenjdk-icedtea-web/package.nix
index 0db3e41bafac..967a38d5c006 100644
--- a/pkgs/development/compilers/adoptopenjdk-icedtea-web/default.nix
+++ b/pkgs/by-name/ad/adoptopenjdk-icedtea-web/package.nix
@@ -5,7 +5,7 @@
   cargo,
   rustc,
   autoreconfHook,
-  jdk,
+  jdk8,
   glib,
   firefox-unwrapped,
   zip,
@@ -14,7 +14,9 @@
   bash,
   bc,
 }:
-
+let
+  jdk = jdk8;
+in
 stdenv.mkDerivation rec {
   pname = "adoptopenjdk-icedtea-web";
 
diff --git a/pkgs/development/compilers/adoptopenjdk-icedtea-web/patches/0001-make-cargo-work-with-nix-build-on-linux.patch b/pkgs/by-name/ad/adoptopenjdk-icedtea-web/patches/0001-make-cargo-work-with-nix-build-on-linux.patch
similarity index 100%
rename from pkgs/development/compilers/adoptopenjdk-icedtea-web/patches/0001-make-cargo-work-with-nix-build-on-linux.patch
rename to pkgs/by-name/ad/adoptopenjdk-icedtea-web/patches/0001-make-cargo-work-with-nix-build-on-linux.patch
diff --git a/pkgs/development/compilers/ballerina/default.nix b/pkgs/by-name/ba/ballerina/package.nix
similarity index 96%
rename from pkgs/development/compilers/ballerina/default.nix
rename to pkgs/by-name/ba/ballerina/package.nix
index 9fa4dcbfdd23..e0c32c309296 100644
--- a/pkgs/development/compilers/ballerina/default.nix
+++ b/pkgs/by-name/ba/ballerina/package.nix
@@ -6,11 +6,12 @@
   makeWrapper,
   fetchzip,
   stdenv,
-  openjdk,
+  openjdk17_headless,
 }:
 let
   version = "2201.10.3";
   codeName = "swan-lake";
+  openjdk = openjdk17_headless;
 in
 stdenv.mkDerivation {
   pname = "ballerina";
diff --git a/pkgs/by-name/bu/burpsuite/package.nix b/pkgs/by-name/bu/burpsuite/package.nix
index bdad64a1ebc8..fb21a68824fe 100644
--- a/pkgs/by-name/bu/burpsuite/package.nix
+++ b/pkgs/by-name/bu/burpsuite/package.nix
@@ -9,20 +9,20 @@
 }:
 
 let
-  version = "2025.9.1";
+  version = "2025.9.3";
 
   product =
     if proEdition then
       {
         productName = "pro";
         productDesktop = "Burp Suite Professional Edition";
-        hash = "sha256-24XijVTFmDshv7TYDW05igUOWfJeHT7z8F8fTCBONoM=";
+        hash = "sha256-gLcSx+AZdHW+LP4kPez1KVamTrp7IfGMF/caHDKAxK4=";
       }
     else
       {
         productName = "community";
         productDesktop = "Burp Suite Community Edition";
-        hash = "sha256-z65+1erFeO3ZOJRGZ+vdbDxfNpo36eIp6yQskItBl1A=";
+        hash = "sha256-LmlmQ6UaIFMGFIFI9r7i9LV81ZcisuNygJo3/oUaWSM=";
       };
 
   src = fetchurl {
diff --git a/pkgs/by-name/ca/cassette/package.nix b/pkgs/by-name/ca/cassette/package.nix
index 7dfe2e770e06..3f0fc3958cff 100644
--- a/pkgs/by-name/ca/cassette/package.nix
+++ b/pkgs/by-name/ca/cassette/package.nix
@@ -24,13 +24,13 @@
 
 stdenv.mkDerivation rec {
   pname = "cassette";
-  version = "0.2.1";
+  version = "0.2.1.g49";
 
   src = fetchFromGitHub {
     owner = "Rirusha";
     repo = "Cassette";
     rev = "v${version}";
-    hash = "sha256-DXCOrCntOgUPYMVRqC4jDNTFgUjShCBoYQgLtSnuz6U=";
+    hash = "sha256-1wIYEDaVlqNDS50MiYGqCtf5xGWou/g/YfZChTdQIns=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/by-name/cp/cpp-utilities/package.nix b/pkgs/by-name/cp/cpp-utilities/package.nix
index a5feb501bb21..92aaba102610 100644
--- a/pkgs/by-name/cp/cpp-utilities/package.nix
+++ b/pkgs/by-name/cp/cpp-utilities/package.nix
@@ -9,13 +9,13 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "cpp-utilities";
-  version = "5.30.0";
+  version = "5.31.0";
 
   src = fetchFromGitHub {
     owner = "Martchus";
     repo = "cpp-utilities";
     rev = "v${finalAttrs.version}";
-    sha256 = "sha256-cBr9Vw0UnC2+x/VSvL8u5hsvgk5RdY/3/KCUFQy24rg=";
+    sha256 = "sha256-UjF1b1LCPwrUzqVZNbtX+5eFAzc6NgLyBzTcNHNlkvs=";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/pkgs/applications/networking/davmail/default.nix b/pkgs/by-name/da/davmail/package.nix
similarity index 93%
rename from pkgs/applications/networking/davmail/default.nix
rename to pkgs/by-name/da/davmail/package.nix
index 9f19363d74fd..c4f3f442cdaa 100644
--- a/pkgs/applications/networking/davmail/default.nix
+++ b/pkgs/by-name/da/davmail/package.nix
@@ -7,18 +7,18 @@
   glib,
   gtk2,
   gtk3,
-  jre,
+  jdk11,
   libXtst,
   coreutils,
   gnugrep,
-  zulu,
+  zulu11,
   preferGtk3 ? true,
   preferZulu ? true,
 }:
 
 let
   rev = 3627;
-  jre' = if preferZulu then zulu else jre;
+  jre' = (if preferZulu then zulu11 else jdk11).override { enableJavaFX = true; };
   gtk' = if preferGtk3 then gtk3 else gtk2;
 in
 stdenv.mkDerivation rec {
diff --git a/pkgs/tools/package-management/disnix/DisnixWebService/default.nix b/pkgs/by-name/di/DisnixWebService/package.nix
similarity index 98%
rename from pkgs/tools/package-management/disnix/DisnixWebService/default.nix
rename to pkgs/by-name/di/DisnixWebService/package.nix
index 5826280a22f6..1a3c64f652c4 100644
--- a/pkgs/tools/package-management/disnix/DisnixWebService/default.nix
+++ b/pkgs/by-name/di/DisnixWebService/package.nix
@@ -4,12 +4,14 @@
   fetchFromGitHub,
   fetchpatch,
   ant,
-  jdk,
+  jdk8,
   xmlstarlet,
   axis2,
   dbus_java,
 }:
-
+let
+  jdk = jdk8;
+in
 stdenv.mkDerivation (finalAttrs: {
   pname = "DisnixWebService";
   version = "0.10.1";
diff --git a/pkgs/servers/elasticmq-server-bin/elasticmq-test.nix b/pkgs/by-name/el/elasticmq-server-bin/elasticmq-test.nix
similarity index 100%
rename from pkgs/servers/elasticmq-server-bin/elasticmq-test.nix
rename to pkgs/by-name/el/elasticmq-server-bin/elasticmq-test.nix
diff --git a/pkgs/servers/elasticmq-server-bin/default.nix b/pkgs/by-name/el/elasticmq-server-bin/package.nix
similarity index 89%
rename from pkgs/servers/elasticmq-server-bin/default.nix
rename to pkgs/by-name/el/elasticmq-server-bin/package.nix
index a02eb7068a47..6b1d2860f4bc 100644
--- a/pkgs/servers/elasticmq-server-bin/default.nix
+++ b/pkgs/by-name/el/elasticmq-server-bin/package.nix
@@ -2,14 +2,17 @@
   lib,
   stdenv,
   fetchurl,
-  jdk,
-  jre,
+  jdk8,
+  jre8,
   makeBinaryWrapper,
   runCommand,
   python3Packages,
   writeText,
 }:
-
+let
+  jre = jre8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
+  jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
+in
 stdenv.mkDerivation (finalAttrs: {
   pname = "elasticmq-server";
   version = "1.6.14";
diff --git a/pkgs/by-name/en/envoy/package.nix b/pkgs/by-name/en/envoy/package.nix
index 131fff6aaf71..a455b4620a37 100644
--- a/pkgs/by-name/en/envoy/package.nix
+++ b/pkgs/by-name/en/envoy/package.nix
@@ -13,7 +13,7 @@
   cmake,
   gn,
   go,
-  jdk,
+  openjdk11_headless,
   ninja,
   patchelf,
   python312,
@@ -56,6 +56,7 @@ let
       .${stdenv.system} or (throw "unsupported system ${stdenv.system}");
 
   python3 = python312;
+  jdk = openjdk11_headless;
 
 in
 buildBazelPackage rec {
diff --git a/pkgs/by-name/en/enzyme/package.nix b/pkgs/by-name/en/enzyme/package.nix
index fa399bd51d45..8558132a7f25 100644
--- a/pkgs/by-name/en/enzyme/package.nix
+++ b/pkgs/by-name/en/enzyme/package.nix
@@ -7,13 +7,13 @@
 }:
 llvmPackages.stdenv.mkDerivation rec {
   pname = "enzyme";
-  version = "0.0.196";
+  version = "0.0.201";
 
   src = fetchFromGitHub {
     owner = "EnzymeAD";
     repo = "Enzyme";
     rev = "v${version}";
-    hash = "sha256-Jrp1DjwMzi8+ZWJVwhZ4SH2phLvrYfY6+29n//z9bUg=";
+    hash = "sha256-TUGWQImDtXOOkEt20719OheKlPgWjEVdqTh/ET/c1cs=";
   };
 
   postPatch = ''
diff --git a/pkgs/by-name/ev/evcc/package.nix b/pkgs/by-name/ev/evcc/package.nix
index ba1087404b22..927b9c5839b3 100644
--- a/pkgs/by-name/ev/evcc/package.nix
+++ b/pkgs/by-name/ev/evcc/package.nix
@@ -17,16 +17,16 @@
 }:
 
 let
-  version = "0.207.6";
+  version = "0.208.1";
 
   src = fetchFromGitHub {
     owner = "evcc-io";
     repo = "evcc";
     tag = version;
-    hash = "sha256-BbX3SXvf6JtWdC5S6jDqBVawMEPtwHBA2IfR5G5ybqA=";
+    hash = "sha256-l7whf2NhvPHZOfXy4PdZq8ZyAKaiLuBlX9s7ffJQoWg=";
   };
 
-  vendorHash = "sha256-ieaDJZmYPxG79Pz/9NRTEhtAQZOqAwwDMa0FAs+PWEA=";
+  vendorHash = "sha256-qp7kSh6pOecXa2qAmKXdJAgAZ4O3pnX0/nMUhwR2cFA=";
 
   commonMeta = with lib; {
     license = licenses.mit;
@@ -52,7 +52,7 @@ buildGo125Module rec {
 
   npmDeps = fetchNpmDeps {
     inherit src;
-    hash = "sha256-GB57pXfWo1lduVDPPw7TBM8qgCmTxPDxKQyD4ZZJnjE=";
+    hash = "sha256-q+ft9dzs/M+ZYCQy/OnqTmpgKXxrD5cfaqrvsxh730w=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/by-name/fr/frigate/package.nix b/pkgs/by-name/fr/frigate/package.nix
index 1fea83763ece..2c40adfc6276 100644
--- a/pkgs/by-name/fr/frigate/package.nix
+++ b/pkgs/by-name/fr/frigate/package.nix
@@ -10,7 +10,6 @@
   frigate,
   nixosTests,
   fetchpatch,
-  protobuf_21,
 }:
 
 let
@@ -41,7 +40,7 @@ let
       });
       onnxruntime = super.onnxruntime.override (old: {
         onnxruntime = old.onnxruntime.override (old: {
-          protobuf = protobuf_21;
+          withFullProtobuf = true;
         });
       });
     };
diff --git a/pkgs/applications/misc/ganttproject-bin/default.nix b/pkgs/by-name/ga/ganttproject-bin/package.nix
similarity index 95%
rename from pkgs/applications/misc/ganttproject-bin/default.nix
rename to pkgs/by-name/ga/ganttproject-bin/package.nix
index 0065eac9c8d5..ab7fbcac624e 100644
--- a/pkgs/applications/misc/ganttproject-bin/default.nix
+++ b/pkgs/by-name/ga/ganttproject-bin/package.nix
@@ -4,9 +4,13 @@
   fetchzip,
   makeDesktopItem,
   makeWrapper,
-  jre,
+  openjdk17,
 }:
-
+let
+  jre = openjdk17.override {
+    enableJavaFX = true;
+  };
+in
 stdenv.mkDerivation rec {
   pname = "ganttproject-bin";
   version = "3.3.3316";
diff --git a/pkgs/by-name/gh/ghostfolio/package.nix b/pkgs/by-name/gh/ghostfolio/package.nix
index 69097113fae4..7322555c2f38 100644
--- a/pkgs/by-name/gh/ghostfolio/package.nix
+++ b/pkgs/by-name/gh/ghostfolio/package.nix
@@ -11,13 +11,13 @@
 
 buildNpmPackage rec {
   pname = "ghostfolio";
-  version = "2.199.0";
+  version = "2.202.0";
 
   src = fetchFromGitHub {
     owner = "ghostfolio";
     repo = "ghostfolio";
     tag = version;
-    hash = "sha256-O21eeTKWwyD029ZuQBKpOE6Y+f9ufSfe70KjxjXQh9M=";
+    hash = "sha256-VBIdNxdAzrlxbNl1p/yv/LUcJhqfD90oZjOsMPKOTDU=";
     # populate values that require us to use git. By doing this in postFetch we
     # can delete .git afterwards and maintain better reproducibility of the src.
     leaveDotGit = true;
@@ -27,7 +27,7 @@ buildNpmPackage rec {
     '';
   };
 
-  npmDepsHash = "sha256-Bo8w+9TySugwAPfUqZHGKBe0hKwvOQIisfA3QENN//s=";
+  npmDepsHash = "sha256-JBes89JG9l+qsrT9g+Rwefe6X7fieQEor5sHpbCEK9Q=";
 
   nativeBuildInputs = [
     prisma
diff --git a/pkgs/applications/editors/greenfoot/default.nix b/pkgs/by-name/gr/greenfoot/package.nix
similarity index 91%
rename from pkgs/applications/editors/greenfoot/default.nix
rename to pkgs/by-name/gr/greenfoot/package.nix
index b2830b4b09d1..5ce999a958d1 100644
--- a/pkgs/applications/editors/greenfoot/default.nix
+++ b/pkgs/by-name/gr/greenfoot/package.nix
@@ -2,12 +2,18 @@
   lib,
   stdenv,
   fetchurl,
-  openjdk,
+  openjdk21,
+  openjfx21,
   glib,
   dpkg,
   wrapGAppsHook3,
 }:
-
+let
+  openjdk = openjdk21.override {
+    enableJavaFX = true;
+    openjfx_jdk = openjfx21.override { withWebKit = true; };
+  };
+in
 stdenv.mkDerivation rec {
   pname = "greenfoot";
   version = "3.9.0";
diff --git a/pkgs/applications/misc/gremlin-console/default.nix b/pkgs/by-name/gr/gremlin-console/package.nix
similarity index 95%
rename from pkgs/applications/misc/gremlin-console/default.nix
rename to pkgs/by-name/gr/gremlin-console/package.nix
index c2c0334a6858..8903b65b6dd9 100644
--- a/pkgs/applications/misc/gremlin-console/default.nix
+++ b/pkgs/by-name/gr/gremlin-console/package.nix
@@ -3,9 +3,11 @@
   lib,
   stdenv,
   makeWrapper,
-  openjdk,
+  openjdk11,
 }:
-
+let
+  openjdk = openjdk11;
+in
 stdenv.mkDerivation rec {
   pname = "gremlin-console";
   version = "3.7.4";
diff --git a/pkgs/applications/misc/gremlin-server/default.nix b/pkgs/by-name/gr/gremlin-server/package.nix
similarity index 96%
rename from pkgs/applications/misc/gremlin-server/default.nix
rename to pkgs/by-name/gr/gremlin-server/package.nix
index 9bf219929151..559470f5dd9c 100644
--- a/pkgs/applications/misc/gremlin-server/default.nix
+++ b/pkgs/by-name/gr/gremlin-server/package.nix
@@ -3,8 +3,11 @@
   lib,
   stdenv,
   makeWrapper,
-  openjdk,
+  openjdk11,
 }:
+let
+  openjdk = openjdk11;
+in
 stdenv.mkDerivation rec {
   pname = "gremlin-server";
   version = "3.7.0";
diff --git a/pkgs/by-name/hi/hired/package.nix b/pkgs/by-name/hi/hired/package.nix
new file mode 100644
index 000000000000..27130e655563
--- /dev/null
+++ b/pkgs/by-name/hi/hired/package.nix
@@ -0,0 +1,49 @@
+{
+  lib,
+  rustPlatform,
+  fetchFromGitHub,
+  nix-update-script,
+  pkg-config,
+  oniguruma,
+}:
+
+rustPlatform.buildRustPackage rec {
+  pname = "hired";
+  version = "0.14.3";
+
+  src = fetchFromGitHub {
+    owner = "sidju";
+    repo = "hired";
+    tag = version;
+    hash = "sha256-A1iz34CSc6GWo6FvkGwIgUwMmYaIzwdCzZFACFSZ9qI=";
+    fetchSubmodules = true;
+  };
+
+  cargoHash = "sha256-nWc3vcqYbJnjYLjKyZQBFR7tSaPaSu0+TvOIBAKKtnQ=";
+
+  nativeBuildInputs = [
+    pkg-config
+  ];
+
+  buildInputs = [
+    oniguruma
+  ];
+
+  env = {
+    RUSTONIG_SYSTEM_LIBONIG = true;
+  };
+
+  enableParallelBuilding = true;
+
+  passthru = {
+    updateScript = nix-update-script { };
+  };
+
+  meta = {
+    description = "Modern take on ed, the standard Unix editor";
+    homepage = "https://github.com/sidju/hired";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ ShamrockLee ];
+    mainProgram = "hired";
+  };
+}
diff --git a/pkgs/applications/audio/ir.lv2/default.nix b/pkgs/by-name/ir/ir-lv2/package.nix
similarity index 100%
rename from pkgs/applications/audio/ir.lv2/default.nix
rename to pkgs/by-name/ir/ir-lv2/package.nix
diff --git a/pkgs/applications/office/jabref/deps.json b/pkgs/by-name/ja/jabref/deps.json
similarity index 100%
rename from pkgs/applications/office/jabref/deps.json
rename to pkgs/by-name/ja/jabref/deps.json
diff --git a/pkgs/applications/office/jabref/default.nix b/pkgs/by-name/ja/jabref/package.nix
similarity index 97%
rename from pkgs/applications/office/jabref/default.nix
rename to pkgs/by-name/ja/jabref/package.nix
index f5c58890e6d0..e94423ed57d1 100644
--- a/pkgs/applications/office/jabref/default.nix
+++ b/pkgs/by-name/ja/jabref/package.nix
@@ -8,11 +8,16 @@
   unzip,
   xdg-utils,
   gtk3,
-  jdk,
+  jdk21,
+  openjfx23,
   gradle_8,
   python3,
 }:
 let
+  jdk = jdk21.override {
+    enableJavaFX = true;
+    openjfx_jdk = openjfx23;
+  };
   # "Deprecated Gradle features were used in this build, making it incompatible with Gradle 9.0."
   gradle = gradle_8;
 in
diff --git a/pkgs/development/libraries/java/cup/javacup-0.11b_beta20160615-build-xml-git.patch b/pkgs/by-name/ja/javaCup/javacup-0.11b_beta20160615-build-xml-git.patch
similarity index 100%
rename from pkgs/development/libraries/java/cup/javacup-0.11b_beta20160615-build-xml-git.patch
rename to pkgs/by-name/ja/javaCup/javacup-0.11b_beta20160615-build-xml-git.patch
diff --git a/pkgs/development/libraries/java/cup/default.nix b/pkgs/by-name/ja/javaCup/package.nix
similarity index 92%
rename from pkgs/development/libraries/java/cup/default.nix
rename to pkgs/by-name/ja/javaCup/package.nix
index 219bbd5908c5..c91666c67808 100644
--- a/pkgs/development/libraries/java/cup/default.nix
+++ b/pkgs/by-name/ja/javaCup/package.nix
@@ -3,11 +3,13 @@
   stdenv,
   fetchurl,
   ant,
-  jdk,
+  jdk8,
   makeWrapper,
   stripJavaArchivesHook,
 }:
-
+let
+  jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
+in
 stdenv.mkDerivation (finalAttrs: {
   pname = "java-cup";
   version = "11b-20160615";
diff --git a/pkgs/development/tools/parsing/javacc/default.nix b/pkgs/by-name/ja/javacc/package.nix
similarity index 84%
rename from pkgs/development/tools/parsing/javacc/default.nix
rename to pkgs/by-name/ja/javacc/package.nix
index a15713456988..9f6f03089afa 100644
--- a/pkgs/development/tools/parsing/javacc/default.nix
+++ b/pkgs/by-name/ja/javacc/package.nix
@@ -3,12 +3,17 @@
   stdenv,
   fetchFromGitHub,
   ant,
-  jdk,
-  jre,
+  jdk8,
+  jre8,
   makeWrapper,
   stripJavaArchivesHook,
 }:
-
+let
+  # Upstream doesn't support anything newer than Java 8.
+  # https://github.com/javacc/javacc/blob/c708628423b71ce8bc3b70143fa5b6a2b7362b3a/README.md#building-javacc-from-source
+  jdk = jdk8;
+  jre = jre8;
+in
 stdenv.mkDerivation (finalAttrs: {
   pname = "javacc";
   version = "7.0.13";
diff --git a/pkgs/by-name/je/jetuml/package.nix b/pkgs/by-name/je/jetuml/package.nix
index e67cba6d2496..d8958de00373 100644
--- a/pkgs/by-name/je/jetuml/package.nix
+++ b/pkgs/by-name/je/jetuml/package.nix
@@ -53,8 +53,8 @@ stdenvNoCC.mkDerivation (finalAttrs: {
     ${jdkWithFX}/lib/openjdk/bin/jar xf $src jet.png
     magick jet.png -resize 128x128 jet128.png
     magick jet.png -resize 48x48 jet48.png
-    install -Dm444 jet48.png $out/share/icons/hicolor/48x48/jet.png
-    install -Dm444 jet128.png $out/share/icons/hicolor/128x128/jet.png
+    install -Dm444 jet48.png $out/share/icons/hicolor/48x48/apps/jet.png
+    install -Dm444 jet128.png $out/share/icons/hicolor/128x128/apps/jet.png
 
     install -Dm444 $src $out/share/java/JetUML-${finalAttrs.version}.jar
 
diff --git a/pkgs/tools/text/xml/jing-trang/no-git-during-build.patch b/pkgs/by-name/ji/jing-trang/no-git-during-build.patch
similarity index 100%
rename from pkgs/tools/text/xml/jing-trang/no-git-during-build.patch
rename to pkgs/by-name/ji/jing-trang/no-git-during-build.patch
diff --git a/pkgs/tools/text/xml/jing-trang/default.nix b/pkgs/by-name/ji/jing-trang/package.nix
similarity index 91%
rename from pkgs/tools/text/xml/jing-trang/default.nix
rename to pkgs/by-name/ji/jing-trang/package.nix
index 4dafa9980a31..d30d0438c4ea 100644
--- a/pkgs/tools/text/xml/jing-trang/default.nix
+++ b/pkgs/by-name/ji/jing-trang/package.nix
@@ -3,11 +3,13 @@
   stdenv,
   fetchFromGitHub,
   jre_headless,
-  jdk_headless,
+  jdk8_headless,
   ant,
   saxon,
 }:
-
+let
+  jdk_headless = jdk8_headless; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
+in
 stdenv.mkDerivation rec {
   pname = "jing-trang";
   version = "20181222";
diff --git a/pkgs/development/tools/java/jprofiler/default.nix b/pkgs/by-name/jp/jprofiler/package.nix
similarity index 99%
rename from pkgs/development/tools/java/jprofiler/default.nix
rename to pkgs/by-name/jp/jprofiler/package.nix
index 753dfddeb2b0..3e380282639a 100644
--- a/pkgs/development/tools/java/jprofiler/default.nix
+++ b/pkgs/by-name/jp/jprofiler/package.nix
@@ -6,10 +6,11 @@
   makeDesktopItem,
   copyDesktopItems,
   _7zz,
-  jdk,
+  jdk11,
 }:
 
 let
+  jdk = jdk11;
   pname = "jprofiler";
   version = "14.0.5";
   nameApp = "JProfiler";
diff --git a/pkgs/applications/misc/keystore-explorer/default.nix b/pkgs/by-name/ke/keystore-explorer/package.nix
similarity index 98%
rename from pkgs/applications/misc/keystore-explorer/default.nix
rename to pkgs/by-name/ke/keystore-explorer/package.nix
index 7aa4aa62910f..6739ab2d1b0e 100644
--- a/pkgs/applications/misc/keystore-explorer/default.nix
+++ b/pkgs/by-name/ke/keystore-explorer/package.nix
@@ -2,12 +2,14 @@
   fetchzip,
   lib,
   stdenv,
-  jdk,
+  jdk11,
   runtimeShell,
   glib,
   wrapGAppsHook3,
 }:
-
+let
+  jdk = jdk11;
+in
 stdenv.mkDerivation rec {
   version = "5.6.0";
   pname = "keystore-explorer";
diff --git a/pkgs/development/libraries/java/libmatthew-java/default.nix b/pkgs/by-name/li/libmatthew_java/package.nix
similarity index 85%
rename from pkgs/development/libraries/java/libmatthew-java/default.nix
rename to pkgs/by-name/li/libmatthew_java/package.nix
index 60bc1231f5ff..83d7fdc2ea26 100644
--- a/pkgs/development/libraries/java/libmatthew-java/default.nix
+++ b/pkgs/by-name/li/libmatthew_java/package.nix
@@ -2,9 +2,11 @@
   lib,
   stdenv,
   fetchurl,
-  jdk,
+  jdk8,
 }:
-
+let
+  jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
+in
 stdenv.mkDerivation rec {
   pname = "libmatthew-java";
   version = "0.8";
diff --git a/pkgs/by-name/lu/luau/package.nix b/pkgs/by-name/lu/luau/package.nix
index dc2d3f80a703..f9b3c5caeaa7 100644
--- a/pkgs/by-name/lu/luau/package.nix
+++ b/pkgs/by-name/lu/luau/package.nix
@@ -9,13 +9,13 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "luau";
-  version = "0.692";
+  version = "0.693";
 
   src = fetchFromGitHub {
     owner = "luau-lang";
     repo = "luau";
     tag = finalAttrs.version;
-    hash = "sha256-GMpSXCiM9QznRAfAsGF+UuzyqS84vGkEy6EZPObRUMk=";
+    hash = "sha256-9D6nIuRP/MyzTYDp7Uo5RcK4QrF+YMV6tTVMX/mAKY8=";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/pkgs/tools/games/minecraft/mcaselector/default.nix b/pkgs/by-name/mc/mcaselector/package.nix
similarity index 90%
rename from pkgs/tools/games/minecraft/mcaselector/default.nix
rename to pkgs/by-name/mc/mcaselector/package.nix
index ffe52140b83d..9336f0c26d22 100644
--- a/pkgs/tools/games/minecraft/mcaselector/default.nix
+++ b/pkgs/by-name/mc/mcaselector/package.nix
@@ -6,7 +6,11 @@
   wrapGAppsHook3,
   jre,
 }:
-
+let
+  jre' = jre.override {
+    enableJavaFX = true;
+  };
+in
 stdenvNoCC.mkDerivation (finalAttrs: {
   pname = "mcaselector";
   version = "2.5.3";
@@ -20,7 +24,7 @@ stdenvNoCC.mkDerivation (finalAttrs: {
   dontBuild = true;
 
   nativeBuildInputs = [
-    jre
+    jre'
     makeWrapper
     wrapGAppsHook3
   ];
@@ -37,7 +41,7 @@ stdenvNoCC.mkDerivation (finalAttrs: {
   '';
 
   preFixup = ''
-    makeWrapper ${jre}/bin/java $out/bin/mcaselector \
+    makeWrapper ${jre'}/bin/java $out/bin/mcaselector \
       --add-flags "-jar $out/lib/mcaselector/mcaselector.jar" \
       ''${gappsWrapperArgs[@]}
   '';
diff --git a/pkgs/applications/audio/melmatcheq.lv2/default.nix b/pkgs/by-name/me/melmatcheq-lv2/package.nix
similarity index 100%
rename from pkgs/applications/audio/melmatcheq.lv2/default.nix
rename to pkgs/by-name/me/melmatcheq-lv2/package.nix
diff --git a/pkgs/by-name/mo/monkeysAudio/package.nix b/pkgs/by-name/mo/monkeysAudio/package.nix
index 3190d4f92171..928ceee0abcf 100644
--- a/pkgs/by-name/mo/monkeysAudio/package.nix
+++ b/pkgs/by-name/mo/monkeysAudio/package.nix
@@ -6,12 +6,12 @@
 }:
 
 stdenv.mkDerivation (finalAttrs: {
-  version = "11.38";
+  version = "11.53";
   pname = "monkeys-audio";
 
   src = fetchzip {
     url = "https://monkeysaudio.com/files/MAC_${builtins.concatStringsSep "" (lib.strings.splitString "." finalAttrs.version)}_SDK.zip";
-    hash = "sha256-/pZeZFyv04Feocm9KfLfItd/z0i3rK7pPf8Jm9jd2c8=";
+    hash = "sha256-g1I63K67upEL0in1NceayLDTQgmx4LAHd0eA0MYEp44=";
     stripRoot = false;
   };
 
diff --git a/pkgs/by-name/mu/muffet/package.nix b/pkgs/by-name/mu/muffet/package.nix
index 3d2a2952e70c..f490fba48285 100644
--- a/pkgs/by-name/mu/muffet/package.nix
+++ b/pkgs/by-name/mu/muffet/package.nix
@@ -2,27 +2,32 @@
   lib,
   buildGoModule,
   fetchFromGitHub,
+  versionCheckHook,
 }:
 
-buildGoModule rec {
+buildGoModule (finalAttrs: {
   pname = "muffet";
   version = "2.11.0";
 
   src = fetchFromGitHub {
     owner = "raviqqe";
     repo = "muffet";
-    rev = "v${version}";
+    tag = "v${finalAttrs.version}";
     hash = "sha256-GfRR+9PdfY63Pzv2XZenKs8XXAKRr9qMzcHOVhl+hv4=";
   };
 
   vendorHash = "sha256-oidOSV8y0VwTabipe7XwurUAra9F65nkTXslwXJ94Jw=";
 
+  doInstallCheck = true;
+  nativeInstallCheckInputs = [ versionCheckHook ];
+  versionCheckProgramArg = "--version";
+
   meta = {
     description = "Website link checker which scrapes and inspects all pages in a website recursively";
     homepage = "https://github.com/raviqqe/muffet";
-    changelog = "https://github.com/raviqqe/muffet/releases/tag/v${version}";
+    changelog = "https://github.com/raviqqe/muffet/releases/tag/${finalAttrs.src.tag}";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ figsoda ];
     mainProgram = "muffet";
   };
-}
+})
diff --git a/pkgs/by-name/nn/nncp/package.nix b/pkgs/by-name/nn/nncp/package.nix
index 8860b501afe3..28a7609bc8da 100644
--- a/pkgs/by-name/nn/nncp/package.nix
+++ b/pkgs/by-name/nn/nncp/package.nix
@@ -12,7 +12,7 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "nncp";
-  version = "8.11.0";
+  version = "8.12.1";
   outputs = [
     "out"
     "doc"
@@ -21,7 +21,7 @@ stdenv.mkDerivation (finalAttrs: {
 
   src = fetchurl {
     url = "http://www.nncpgo.org/download/nncp-${finalAttrs.version}.tar.xz";
-    hash = "sha256-7EEUvNkYSqh4HzjbqjqgQlXfu6nDU2v3WWnma8M0r/I=";
+    hash = "sha256-yTwndQ43aBCned7iKPZm70zCC3zMapf2GXtornjiZos=";
   };
 
   nativeBuildInputs = [
@@ -36,7 +36,7 @@ stdenv.mkDerivation (finalAttrs: {
 
   buildPhase = ''
     runHook preBuild
-    ./bin/build
+    ./build
     runHook postBuild
   '';
 
diff --git a/pkgs/by-name/on/onnxruntime/package.nix b/pkgs/by-name/on/onnxruntime/package.nix
index 2964c8a1ac37..9bd15499960e 100644
--- a/pkgs/by-name/on/onnxruntime/package.nix
+++ b/pkgs/by-name/on/onnxruntime/package.nix
@@ -23,6 +23,7 @@
   pythonSupport ? true,
   cudaSupport ? config.cudaSupport,
   ncclSupport ? config.cudaSupport,
+  withFullProtobuf ? false,
   cudaPackages ? { },
 }@inputs:
 
@@ -195,7 +196,7 @@ effectiveStdenv.mkDerivation rec {
     (lib.cmakeFeature "ONNX_CUSTOM_PROTOC_EXECUTABLE" (lib.getExe protobuf))
     (lib.cmakeBool "onnxruntime_BUILD_SHARED_LIB" true)
     (lib.cmakeBool "onnxruntime_BUILD_UNIT_TESTS" doCheck)
-    (lib.cmakeBool "onnxruntime_USE_FULL_PROTOBUF" false)
+    (lib.cmakeBool "onnxruntime_USE_FULL_PROTOBUF" withFullProtobuf)
     (lib.cmakeBool "onnxruntime_USE_CUDA" cudaSupport)
     (lib.cmakeBool "onnxruntime_USE_NCCL" (cudaSupport && ncclSupport))
     (lib.cmakeBool "onnxruntime_ENABLE_LTO" (!cudaSupport || cudaPackages.cudaOlder "12.8"))
diff --git a/pkgs/tools/networking/openapi-generator-cli/example.nix b/pkgs/by-name/op/openapi-generator-cli/example.nix
similarity index 100%
rename from pkgs/tools/networking/openapi-generator-cli/example.nix
rename to pkgs/by-name/op/openapi-generator-cli/example.nix
diff --git a/pkgs/tools/networking/openapi-generator-cli/default.nix b/pkgs/by-name/op/openapi-generator-cli/package.nix
similarity index 97%
rename from pkgs/tools/networking/openapi-generator-cli/default.nix
rename to pkgs/by-name/op/openapi-generator-cli/package.nix
index 21981d09e435..87968f9980ef 100644
--- a/pkgs/tools/networking/openapi-generator-cli/default.nix
+++ b/pkgs/by-name/op/openapi-generator-cli/package.nix
@@ -3,11 +3,12 @@
   lib,
   stdenv,
   fetchurl,
-  jre,
+  jre_headless,
   makeWrapper,
 }:
 
 let
+  jre = jre_headless;
   this = stdenv.mkDerivation (finalAttrs: {
     version = "7.15.0";
     pname = "openapi-generator-cli";
diff --git a/pkgs/by-name/op/opencollada-blender/cmake4-compat.patch b/pkgs/by-name/op/opencollada-blender/cmake4-compat.patch
new file mode 100644
index 000000000000..c586a589534a
--- /dev/null
+++ b/pkgs/by-name/op/opencollada-blender/cmake4-compat.patch
@@ -0,0 +1,26 @@
+From f036950f1ccc3ebdfe2fdc0a52d35a4620252901 Mon Sep 17 00:00:00 2001
+From: Grimmauld <Grimmauld@grimmauld.de>
+Date: Sat, 27 Sep 2025 11:43:21 +0200
+Subject: [PATCH] Build: update cmake minimum version to 3.10
+
+cmake ABI compatibility with cmake <3.5 has been removed in cmake 4.
+Compatibility with cmake <3.10 is deprecated and soon to be removed.
+Thus set 3.10 minimum version. This is available in the vast majority
+of current linux distributions, as well as other platforms.
+---
+ CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 95abbe213..2d14b2552 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -18,7 +18,7 @@ if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
+ 	endif()
+ endif()
+ 
+-cmake_minimum_required(VERSION 2.6)
++cmake_minimum_required(VERSION 3.10)
+ 
+ 
+ #-----------------------------------------------------------------------------
diff --git a/pkgs/by-name/op/opencollada-blender/package.nix b/pkgs/by-name/op/opencollada-blender/package.nix
index 1fa9ebb2703b..01042195cd9a 100644
--- a/pkgs/by-name/op/opencollada-blender/package.nix
+++ b/pkgs/by-name/op/opencollada-blender/package.nix
@@ -1,5 +1,6 @@
 {
   cmake,
+  dos2unix,
   fetchFromGitHub,
   lib,
   libxml2,
@@ -19,9 +20,20 @@ stdenv.mkDerivation {
     sha256 = "sha256-ctr+GjDzxOJxBfaMwjwayPkAOcF+FMsP1X72QCOwvTY=";
   };
 
+  # Fix freaky dos-style CLRF things
+  prePatch = ''
+    dos2unix CMakeLists.txt
+  '';
+
+  patches = [
+    # https://github.com/aras-p/OpenCOLLADA/pull/1
+    ./cmake4-compat.patch
+  ];
+
   nativeBuildInputs = [
     cmake
     pkg-config
+    dos2unix
   ];
 
   propagatedBuildInputs = [
@@ -31,7 +43,7 @@ stdenv.mkDerivation {
 
   meta = {
     description = "Library for handling the COLLADA file format";
-    homepage = "https://github.com/KhronosGroup/OpenCOLLADA/";
+    homepage = "https://github.com/aras-p/OpenCOLLADA";
     maintainers = [ lib.maintainers.amarshall ];
     platforms = lib.platforms.unix;
     license = lib.licenses.mit;
diff --git a/pkgs/applications/science/misc/openrefine/default.nix b/pkgs/by-name/op/openrefine/package.nix
similarity index 99%
rename from pkgs/applications/science/misc/openrefine/default.nix
rename to pkgs/by-name/op/openrefine/package.nix
index 22852f99116c..d9ea9e4270e1 100644
--- a/pkgs/applications/science/misc/openrefine/default.nix
+++ b/pkgs/by-name/op/openrefine/package.nix
@@ -4,13 +4,14 @@
   fetchFromGitHub,
   buildNpmPackage,
   curl,
-  jdk,
+  jdk17,
   jq,
   makeWrapper,
   maven,
 }:
 
 let
+  jdk = jdk17;
   version = "3.9.5";
   src = fetchFromGitHub {
     owner = "openrefine";
diff --git a/pkgs/applications/science/misc/openrefine/update.sh b/pkgs/by-name/op/openrefine/update.sh
similarity index 100%
rename from pkgs/applications/science/misc/openrefine/update.sh
rename to pkgs/by-name/op/openrefine/update.sh
diff --git a/pkgs/applications/misc/pattypan/default.nix b/pkgs/by-name/pa/pattypan/package.nix
similarity index 94%
rename from pkgs/applications/misc/pattypan/default.nix
rename to pkgs/by-name/pa/pattypan/package.nix
index a02c8ae92f53..7145f56a9289 100644
--- a/pkgs/applications/misc/pattypan/default.nix
+++ b/pkgs/by-name/pa/pattypan/package.nix
@@ -10,7 +10,9 @@
   copyDesktopItems,
   stripJavaArchivesHook,
 }:
-
+let
+  jdk' = jdk.override { enableJavaFX = true; };
+in
 stdenv.mkDerivation (finalAttrs: {
   pname = "pattypan";
   version = "22.03";
@@ -50,7 +52,7 @@ stdenv.mkDerivation (finalAttrs: {
 
   # gappsWrapperArgs is set in preFixup
   postFixup = ''
-    makeWrapper ${jdk}/bin/java $out/bin/pattypan \
+    makeWrapper ${jdk'}/bin/java $out/bin/pattypan \
         ''${gappsWrapperArgs[@]} \
         --add-flags "-jar $out/share/pattypan/pattypan.jar"
   '';
diff --git a/pkgs/applications/graphics/processing/disable-revision-check.patch b/pkgs/by-name/pr/processing/disable-revision-check.patch
similarity index 100%
rename from pkgs/applications/graphics/processing/disable-revision-check.patch
rename to pkgs/by-name/pr/processing/disable-revision-check.patch
diff --git a/pkgs/applications/graphics/processing/default.nix b/pkgs/by-name/pr/processing/package.nix
similarity index 99%
rename from pkgs/applications/graphics/processing/default.nix
rename to pkgs/by-name/pr/processing/package.nix
index 65e28fec764a..7f595dc48c56 100644
--- a/pkgs/applications/graphics/processing/default.nix
+++ b/pkgs/by-name/pr/processing/package.nix
@@ -6,7 +6,7 @@
   ant,
   unzip,
   makeWrapper,
-  jdk,
+  jdk17,
   jogl,
   rsync,
   ffmpeg,
@@ -16,6 +16,7 @@
   libGL,
 }:
 let
+  jdk = jdk17;
   buildNumber = "1295";
   vaqua = fetchurl {
     name = "VAqua9.jar";
diff --git a/pkgs/by-name/py/pyradio/package.nix b/pkgs/by-name/py/pyradio/package.nix
index b8ded4722ed7..38f39b35f89e 100644
--- a/pkgs/by-name/py/pyradio/package.nix
+++ b/pkgs/by-name/py/pyradio/package.nix
@@ -7,14 +7,14 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "pyradio";
-  version = "0.9.3.11.18";
+  version = "0.9.3.11.19";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "coderholic";
     repo = "pyradio";
     tag = version;
-    hash = "sha256-/JUNA3gbnmJBFMVxffSmbngiHRlzjzMHCPTfJq0TqLA=";
+    hash = "sha256-fjTaURYY2pSb3mod4Vffbczmyxsn0/4SAXkb68mRhQA=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/development/tools/scalafix/default.nix b/pkgs/by-name/sc/scalafix/package.nix
similarity index 94%
rename from pkgs/development/tools/scalafix/default.nix
rename to pkgs/by-name/sc/scalafix/package.nix
index 94abffd96120..9aa101f331de 100644
--- a/pkgs/development/tools/scalafix/default.nix
+++ b/pkgs/by-name/sc/scalafix/package.nix
@@ -1,13 +1,16 @@
 {
   lib,
   stdenv,
-  jre,
+  jre8,
   coursier,
   makeWrapper,
   installShellFiles,
   setJavaClassPath,
   testers,
 }:
+let
+  jre = jre8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
+in
 stdenv.mkDerivation (finalAttrs: {
   pname = "scalafix";
   version = "0.12.0";
diff --git a/pkgs/by-name/sc/scalapack/package.nix b/pkgs/by-name/sc/scalapack/package.nix
index 6dfbf1891946..408337773ba7 100644
--- a/pkgs/by-name/sc/scalapack/package.nix
+++ b/pkgs/by-name/sc/scalapack/package.nix
@@ -80,7 +80,7 @@ stdenv.mkDerivation (finalAttrs: {
   # this line is left so those who force installation on x86_64-darwin can still build
   doCheck = !(stdenv.hostPlatform.isx86_64 && stdenv.hostPlatform.isDarwin);
 
-  cmakeFlagsArray = [
+  cmakeFlags = [
     (lib.cmakeBool "BUILD_SHARED_LIBS" (!stdenv.hostPlatform.isStatic))
     (lib.cmakeFeature "LAPACK_LIBRARIES" "-llapack")
     (lib.cmakeFeature "BLAS_LIBRARIES" "-lblas")
@@ -102,7 +102,7 @@ stdenv.mkDerivation (finalAttrs: {
     # cmake file will thus look for the library in the dev output instead of out.
     # Use the absolute path to $out instead to fix the issue.
     substituteInPlace  $dev/lib/cmake/scalapack-${finalAttrs.version}/scalapack-targets-release.cmake \
-      --replace "\''${_IMPORT_PREFIX}" "$out"
+      --replace-fail "\''${_IMPORT_PREFIX}" "$out"
   '';
 
   meta = {
diff --git a/pkgs/tools/games/slipstream/default.nix b/pkgs/by-name/sl/slipstream/package.nix
similarity index 98%
rename from pkgs/tools/games/slipstream/default.nix
rename to pkgs/by-name/sl/slipstream/package.nix
index 8269072876f3..2911890df5aa 100644
--- a/pkgs/tools/games/slipstream/default.nix
+++ b/pkgs/by-name/sl/slipstream/package.nix
@@ -3,9 +3,11 @@
   fetchFromGitHub,
   makeWrapper,
   maven,
-  jdk,
+  jdk8,
 }:
-
+let
+  jdk = jdk8;
+in
 maven.buildMavenPackage rec {
   pname = "slipstream";
   version = "1.9.1";
diff --git a/pkgs/by-name/sn/snx-rs/package.nix b/pkgs/by-name/sn/snx-rs/package.nix
index 3707b4520d8a..eb2ebac90e52 100644
--- a/pkgs/by-name/sn/snx-rs/package.nix
+++ b/pkgs/by-name/sn/snx-rs/package.nix
@@ -14,13 +14,13 @@
 }:
 rustPlatform.buildRustPackage rec {
   pname = "snx-rs";
-  version = "4.8.0";
+  version = "4.8.1";
 
   src = fetchFromGitHub {
     owner = "ancwrd1";
     repo = "snx-rs";
     tag = "v${version}";
-    hash = "sha256-D2WVmu+vECabVdnJtc7ihlj83Z/2m6kD8KZ9ot9dCRE=";
+    hash = "sha256-/ntw1AuOqTy9s1jY+6UIDqZWtmjr1DVRQur/h0LkkXI=";
   };
 
   passthru.updateScript = nix-update-script { };
@@ -47,7 +47,7 @@ rustPlatform.buildRustPackage rec {
     versionCheckHook
   ];
 
-  cargoHash = "sha256-+rTpuAe+6YdgCQr/+zJMaSYo4T+3Fkma0PSVjnsxAfg=";
+  cargoHash = "sha256-lLYQ+N5P8p4jiJCo6UyXvXeDT9JRlzIk8VH6UKlqvX0=";
 
   doInstallCheck = true;
   versionCheckProgram = "${placeholder "out"}/bin/snx-rs";
diff --git a/pkgs/applications/networking/soapui/default.nix b/pkgs/by-name/so/soapui/package.nix
similarity index 100%
rename from pkgs/applications/networking/soapui/default.nix
rename to pkgs/by-name/so/soapui/package.nix
diff --git a/pkgs/applications/audio/tamgamp.lv2/default.nix b/pkgs/by-name/ta/tamgamp-lv2/package.nix
similarity index 100%
rename from pkgs/applications/audio/tamgamp.lv2/default.nix
rename to pkgs/by-name/ta/tamgamp-lv2/package.nix
diff --git a/pkgs/by-name/ti/timg/package.nix b/pkgs/by-name/ti/timg/package.nix
index bc9206b1af25..ffe8b6cdb6b4 100644
--- a/pkgs/by-name/ti/timg/package.nix
+++ b/pkgs/by-name/ti/timg/package.nix
@@ -20,13 +20,13 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "timg";
-  version = "1.6.2";
+  version = "1.6.3";
 
   src = fetchFromGitHub {
     owner = "hzeller";
     repo = "timg";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-UiQ8CW0mxjjQM6XLN0FL2v7ccYq2EmIy/3pm+yKQh8w=";
+    hash = "sha256-FdaO+UAKjmLKgVZ3AYGQ9VJQj9s48Ihr8TlZ4at5I3c=";
   };
 
   buildInputs = [
diff --git a/pkgs/applications/science/biology/trimmomatic/default.nix b/pkgs/by-name/tr/trimmomatic/package.nix
similarity index 89%
rename from pkgs/applications/science/biology/trimmomatic/default.nix
rename to pkgs/by-name/tr/trimmomatic/package.nix
index 1c22b3ec7fb3..c3285d2be4bd 100644
--- a/pkgs/applications/science/biology/trimmomatic/default.nix
+++ b/pkgs/by-name/tr/trimmomatic/package.nix
@@ -3,12 +3,22 @@
   stdenv,
   fetchFromGitHub,
   ant,
-  jdk,
-  jre,
+  jdk21_headless,
+  jre_minimal,
   makeWrapper,
   stripJavaArchivesHook,
 }:
-
+let
+  jdk = jdk21_headless;
+  # Reduce closure size
+  jre = jre_minimal.override {
+    modules = [
+      "java.base"
+      "java.logging"
+    ];
+    jdk = jdk21_headless;
+  };
+in
 stdenv.mkDerivation (finalAttrs: {
   pname = "trimmomatic";
   version = "0.39";
diff --git a/pkgs/by-name/vo/volanta/package.nix b/pkgs/by-name/vo/volanta/package.nix
index 4049740295cd..4ca71b69efc3 100644
--- a/pkgs/by-name/vo/volanta/package.nix
+++ b/pkgs/by-name/vo/volanta/package.nix
@@ -9,11 +9,11 @@
 }:
 let
   pname = "volanta";
-  version = "1.13.2";
-  build = "946a5f81";
+  version = "1.13.3";
+  build = "cdb350c9";
   src = fetchurl {
     url = "https://cdn.volanta.app/software/volanta-app/${version}-${build}/volanta-${version}.AppImage";
-    hash = "sha256-kY+z/6G0XbnO5YctCSQobBG0mQee/ODKvh6sUg6H+ZU=";
+    hash = "sha256-0q0ShXqN1xA4+bKOX5jebUV+pDh+BNok5WZLLPrq0ks=";
   };
   appImageContents = appimageTools.extract { inherit pname version src; };
 in
diff --git a/pkgs/by-name/vu/vue-language-server/package.nix b/pkgs/by-name/vu/vue-language-server/package.nix
index 445a7453d89d..2bd4318e40d3 100644
--- a/pkgs/by-name/vu/vue-language-server/package.nix
+++ b/pkgs/by-name/vu/vue-language-server/package.nix
@@ -37,7 +37,6 @@ stdenv.mkDerivation (finalAttrs: {
   '';
 
   preInstall = ''
-    CI=true pnpm prune --prod
     find -type f \( -name "*.ts" -o -name "*.map" \) -exec rm -rf {} +
 
     # https://github.com/pnpm/pnpm/issues/3645
diff --git a/pkgs/by-name/xe/xemu/package.nix b/pkgs/by-name/xe/xemu/package.nix
index c1495c60eab2..ca7657878884 100644
--- a/pkgs/by-name/xe/xemu/package.nix
+++ b/pkgs/by-name/xe/xemu/package.nix
@@ -32,13 +32,13 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "xemu";
-  version = "0.8.98";
+  version = "0.8.105";
 
   src = fetchFromGitHub {
     owner = "xemu-project";
     repo = "xemu";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-kqNZFRkLZ7MiniV2kg+FJ6E4Ms/8+pQLHe8MvhZYC0I=";
+    hash = "sha256-1Gp/XGPCIT8qeW1YPI+mh6P0avHHFXtOGcXEEkGT12w=";
 
     nativeBuildInputs = [
       git
diff --git a/pkgs/by-name/xm/xmloscopy/package.nix b/pkgs/by-name/xm/xmloscopy/package.nix
index faab84dc3cef..e0df62513ddd 100644
--- a/pkgs/by-name/xm/xmloscopy/package.nix
+++ b/pkgs/by-name/xm/xmloscopy/package.nix
@@ -9,7 +9,7 @@
   coreutils,
   libxml2,
   libxslt,
-  jing,
+  jing-trang,
   findutils,
   gnugrep,
   gnused,
@@ -29,7 +29,7 @@ stdenv.mkDerivation rec {
     coreutils
     libxml2
     libxslt
-    jing
+    jing-trang
     findutils
     gnugrep
     gnused
diff --git a/pkgs/by-name/yo/yourkit-java/package.nix b/pkgs/by-name/yo/yourkit-java/package.nix
index 6b92b70900ca..b19d6e752f6d 100644
--- a/pkgs/by-name/yo/yourkit-java/package.nix
+++ b/pkgs/by-name/yo/yourkit-java/package.nix
@@ -5,9 +5,11 @@
   copyDesktopItems,
   imagemagick,
   makeDesktopItem,
-  jre,
+  jdk21,
 }:
 let
+  jre = jdk21;
+
   vPath = v: lib.elemAt (lib.splitString "-" v) 0;
 
   version = "2025.3-b154";
diff --git a/pkgs/development/compilers/abcl/default.nix b/pkgs/development/compilers/abcl/default.nix
index bc00e173ac24..a030be518b7c 100644
--- a/pkgs/development/compilers/abcl/default.nix
+++ b/pkgs/development/compilers/abcl/default.nix
@@ -4,12 +4,16 @@
   writeShellScriptBin,
   fetchurl,
   ant,
-  jdk,
+  openjdk17,
   makeWrapper,
   stripJavaArchivesHook,
 }:
 
 let
+  # https://armedbear.common-lisp.dev/ lists OpenJDK 17 as the highest
+  # supported JDK.
+  jdk = openjdk17;
+
   fakeHostname = writeShellScriptBin "hostname" ''
     echo nix-builder.localdomain
   '';
diff --git a/pkgs/development/interpreters/clojure/default.nix b/pkgs/development/interpreters/clojure/default.nix
index 438331140b41..7a0bdcf58860 100644
--- a/pkgs/development/interpreters/clojure/default.nix
+++ b/pkgs/development/interpreters/clojure/default.nix
@@ -4,12 +4,15 @@
   bashNonInteractive,
   fetchurl,
   installShellFiles,
-  jdk,
+  jdk21,
   rlwrap,
   makeWrapper,
   writeScript,
 }:
-
+let
+  # set this to an LTS version of java
+  jdk = jdk21;
+in
 stdenv.mkDerivation (finalAttrs: {
   pname = "clojure";
   version = "1.12.2.1565";
diff --git a/pkgs/development/libraries/fmt/default.nix b/pkgs/development/libraries/fmt/default.nix
index ed928af31cb5..a88e41c95873 100644
--- a/pkgs/development/libraries/fmt/default.nix
+++ b/pkgs/development/libraries/fmt/default.nix
@@ -62,7 +62,7 @@ let
         homepage = "https://fmt.dev/";
         changelog = "https://github.com/fmtlib/fmt/blob/${version}/ChangeLog.rst";
         downloadPage = "https://github.com/fmtlib/fmt/";
-        maintainers = [ maintainers.jdehaas ];
+        maintainers = [ ];
         license = licenses.mit;
         platforms = platforms.all;
       };
diff --git a/pkgs/development/libraries/qtutilities/default.nix b/pkgs/development/libraries/qtutilities/default.nix
index f1e07e9d6397..c33658cc59b7 100644
--- a/pkgs/development/libraries/qtutilities/default.nix
+++ b/pkgs/development/libraries/qtutilities/default.nix
@@ -10,13 +10,13 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "qtutilities";
-  version = "6.18.1";
+  version = "6.18.2";
 
   src = fetchFromGitHub {
     owner = "Martchus";
     repo = "qtutilities";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-GFLNZgY6Q3+4lsFYznbiVhDqU8ALzVRLO02qmyZrnKw=";
+    hash = "sha256-SwKXON16a9qmI+FrTA1OH0zIqf5rfAWbGOhCpCIHgr4=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/development/python-modules/amazon-ion/default.nix b/pkgs/development/python-modules/amazon-ion/default.nix
index a7569cd5d06a..0d4a9bd1578b 100644
--- a/pkgs/development/python-modules/amazon-ion/default.nix
+++ b/pkgs/development/python-modules/amazon-ion/default.nix
@@ -6,7 +6,7 @@
   fetchFromGitHub,
   jsonconversion,
   pytestCheckHook,
-  pythonOlder,
+  pytest_7,
   setuptools,
   six,
   tabulate,
@@ -17,8 +17,6 @@ buildPythonPackage rec {
   version = "0.13.0";
   pyproject = true;
 
-  disabled = pythonOlder "3.7";
-
   src = fetchFromGitHub {
     owner = "amazon-ion";
     repo = "ion-python";
@@ -33,9 +31,9 @@ buildPythonPackage rec {
       --replace "'pytest-runner'," ""
   '';
 
-  nativeBuildInputs = [ setuptools ];
+  build-system = [ setuptools ];
 
-  propagatedBuildInputs = [
+  dependencies = [
     jsonconversion
     six
   ];
@@ -43,7 +41,7 @@ buildPythonPackage rec {
   nativeCheckInputs = [
     cbor2
     docopt
-    pytestCheckHook
+    (pytestCheckHook.override { pytest = pytest_7; })
     tabulate
   ];
 
diff --git a/pkgs/development/python-modules/asyncpraw/default.nix b/pkgs/development/python-modules/asyncpraw/default.nix
index 5435eb099e46..0126f99cc91e 100644
--- a/pkgs/development/python-modules/asyncpraw/default.nix
+++ b/pkgs/development/python-modules/asyncpraw/default.nix
@@ -9,7 +9,7 @@
   flit-core,
   mock,
   pytestCheckHook,
-  pytest-asyncio,
+  pytest-asyncio_0,
   pytest-vcr,
   pythonOlder,
   requests-toolbelt,
@@ -49,7 +49,7 @@ buildPythonPackage rec {
 
   nativeCheckInputs = [
     pytestCheckHook
-    pytest-asyncio
+    pytest-asyncio_0
     pytest-vcr
     vcrpy
     requests-toolbelt
diff --git a/pkgs/development/python-modules/asyncprawcore/default.nix b/pkgs/development/python-modules/asyncprawcore/default.nix
index 133d74aefb7c..bc8c34f86a01 100644
--- a/pkgs/development/python-modules/asyncprawcore/default.nix
+++ b/pkgs/development/python-modules/asyncprawcore/default.nix
@@ -6,9 +6,8 @@
   flit-core,
   mock,
   pytestCheckHook,
-  pytest-asyncio,
+  pytest-asyncio_0,
   pytest-vcr,
-  pythonOlder,
   requests,
   requests-toolbelt,
   testfixtures,
@@ -21,8 +20,6 @@ buildPythonPackage rec {
   version = "2.4.0";
   pyproject = true;
 
-  disabled = pythonOlder "3.8";
-
   src = fetchFromGitHub {
     owner = "praw-dev";
     repo = "asyncprawcore";
@@ -30,9 +27,9 @@ buildPythonPackage rec {
     hash = "sha256-FDQdtnNjsbiEp9BUYdQFMC/hkyJDhCh2WHhQWSQwrFY=";
   };
 
-  nativeBuildInputs = [ flit-core ];
+  build-system = [ flit-core ];
 
-  propagatedBuildInputs = [
+  dependencies = [
     requests
     aiohttp
     yarl
@@ -43,7 +40,7 @@ buildPythonPackage rec {
     mock
     requests-toolbelt
     pytestCheckHook
-    pytest-asyncio
+    pytest-asyncio_0
     pytest-vcr
     vcrpy
   ];
diff --git a/pkgs/development/python-modules/asyncua/default.nix b/pkgs/development/python-modules/asyncua/default.nix
index 6e77e4b1d1b2..f208334661a6 100644
--- a/pkgs/development/python-modules/asyncua/default.nix
+++ b/pkgs/development/python-modules/asyncua/default.nix
@@ -6,6 +6,7 @@
   buildPythonPackage,
   cryptography,
   fetchFromGitHub,
+  hatchling,
   pyopenssl,
   pytest-asyncio_0_21,
   pytest-mock,
@@ -14,7 +15,6 @@
   pythonAtLeast,
   pythonOlder,
   pytz,
-  setuptools,
   sortedcontainers,
   typing-extensions,
 }:
@@ -41,7 +41,7 @@ buildPythonPackage rec {
       --replace-fail "tools/" "$out/bin/"
   '';
 
-  build-system = [ setuptools ];
+  build-system = [ hatchling ];
 
   dependencies = [
     aiofiles
diff --git a/pkgs/development/python-modules/awswrangler/default.nix b/pkgs/development/python-modules/awswrangler/default.nix
index ef33e99adc91..1f73e157b64f 100644
--- a/pkgs/development/python-modules/awswrangler/default.nix
+++ b/pkgs/development/python-modules/awswrangler/default.nix
@@ -1,41 +1,38 @@
 {
-  sparqlwrapper,
+  lib,
   boto3,
   buildPythonPackage,
   fetchFromGitHub,
   gremlinpython,
+  hatchling,
   jsonpath-ng,
-  lib,
   moto,
   openpyxl,
   opensearch-py,
   pandas,
   pg8000,
-  poetry-core,
   progressbar2,
   pyarrow,
   pymysql,
   pyodbc,
   pyparsing,
   pytestCheckHook,
-  pythonOlder,
   redshift-connector,
   requests-aws4auth,
   setuptools,
+  sparqlwrapper,
 }:
 
 buildPythonPackage rec {
   pname = "awswrangler";
-  version = "3.12.1";
+  version = "3.13.0";
   pyproject = true;
 
-  disabled = pythonOlder "3.8";
-
   src = fetchFromGitHub {
     owner = "aws";
     repo = "aws-sdk-pandas";
     tag = version;
-    hash = "sha256-N4IqeAfW4PqgQcBFaFK/Ugbcsz8pLiFzkBr9SRm7AOs=";
+    hash = "sha256-MkoJpztVjwZbGcJTdnLRF7ZtIFd0qGoz/cksEoqLe4w=";
   };
 
   pythonRelaxDeps = [
@@ -43,7 +40,7 @@ buildPythonPackage rec {
     "pyarrow"
   ];
 
-  build-system = [ poetry-core ];
+  build-system = [ hatchling ];
 
   dependencies = [
     boto3
diff --git a/pkgs/development/python-modules/binsync/default.nix b/pkgs/development/python-modules/binsync/default.nix
index 7883e9b5ed42..3f6c999a6668 100644
--- a/pkgs/development/python-modules/binsync/default.nix
+++ b/pkgs/development/python-modules/binsync/default.nix
@@ -14,6 +14,7 @@
   sortedcontainers,
   toml,
   tqdm,
+  wordfreq,
 }:
 
 buildPythonPackage rec {
@@ -39,6 +40,7 @@ buildPythonPackage rec {
     sortedcontainers
     toml
     tqdm
+    wordfreq
   ];
 
   optional-dependencies = {
@@ -52,7 +54,7 @@ buildPythonPackage rec {
   ];
 
   disabledTestPaths = [
-    # Test tries to import angrmanagement
+    # Test tries to import angr-management
     "tests/test_angr_gui.py"
   ];
 
diff --git a/pkgs/development/python-modules/celery-redbeat/default.nix b/pkgs/development/python-modules/celery-redbeat/default.nix
index c8d04153df73..cd5be7937ee2 100644
--- a/pkgs/development/python-modules/celery-redbeat/default.nix
+++ b/pkgs/development/python-modules/celery-redbeat/default.nix
@@ -1,48 +1,64 @@
 {
   lib,
   buildPythonPackage,
-  fetchFromGitHub,
-  python-dateutil,
   celery,
-  redis,
-  tenacity,
-  pytestCheckHook,
-  pytz,
+  cron-descriptor,
+  django-timezone-field,
+  django,
   fakeredis,
+  fetchFromGitHub,
   mock,
+  pytestCheckHook,
+  python-crontab,
+  python-dateutil,
+  pytz,
+  setuptools,
 }:
 
 buildPythonPackage rec {
   pname = "celery-redbeat";
-  version = "2.3.3";
-  format = "setuptools";
+  version = "2.8.1";
+  pyproject = true;
 
   src = fetchFromGitHub {
-    owner = "sibson";
-    repo = "redbeat";
+    owner = "celery";
+    repo = "django-celery-beat";
     tag = "v${version}";
-    hash = "sha256-bptEAOVxuwj9Y7LyBhtMU22Z1uCiJ4O4BZT2ytqQI80=";
+    hash = "sha256-pakOpch5r2ug0UDSqEU34qr4Tz1/mkuFiHW+IOUuGcc=";
   };
 
-  propagatedBuildInputs = [
+  postPatch = ''
+    # Hack the custom dependency resolution in setup.py to avoid pulling in pip
+    substituteInPlace setup.py \
+      --replace-fail "install_requires=reqs('default.txt') + reqs('runtime.txt')," "install_requires=[],"
+  '';
+
+  build-system = [ setuptools ];
+
+  dependencies = [
     celery
+    cron-descriptor
+    django
+    django-timezone-field
+    python-crontab
     python-dateutil
-    redis
-    tenacity
   ];
 
   nativeCheckInputs = [
-    fakeredis
     mock
     pytestCheckHook
     pytz
   ];
 
-  pythonImportsCheck = [ "redbeat" ];
+  pythonImportsCheck = [ "django_celery_beat" ];
+
+  # Tests require additional work
+  doCheck = false;
 
   meta = with lib; {
     description = "Database-backed Periodic Tasks";
     homepage = "https://github.com/celery/django-celery-beat";
+    changelog = "https://github.com/celery/django-celery-beat/releases/tag/${src.tag}";
     license = licenses.bsd3;
     maintainers = with maintainers; [ onny ];
   };
diff --git a/pkgs/development/python-modules/control/default.nix b/pkgs/development/python-modules/control/default.nix
index 16bb10a94ea0..4f766f00fcbd 100644
--- a/pkgs/development/python-modules/control/default.nix
+++ b/pkgs/development/python-modules/control/default.nix
@@ -1,15 +1,16 @@
 {
   lib,
-  fetchFromGitHub,
   buildPythonPackage,
-  numpy,
-  scipy,
-  matplotlib,
-  setuptools,
-  setuptools-scm,
   cvxopt,
+  fetchFromGitHub,
+  matplotlib,
+  numpy,
+  numpydoc,
   pytest-timeout,
   pytestCheckHook,
+  scipy,
+  setuptools-scm,
+  setuptools,
 }:
 
 buildPythonPackage rec {
@@ -41,17 +42,23 @@ buildPythonPackage rec {
     cvxopt = [ cvxopt ];
   };
 
-  pythonImportsCheck = [ "control" ];
-
   nativeCheckInputs = [
-    cvxopt
+    numpydoc
     pytest-timeout
     pytestCheckHook
+  ]
+  ++ lib.flatten (builtins.attrValues optional-dependencies);
+
+  pythonImportsCheck = [ "control" ];
+
+  disabledTestPaths = [
+    # Don't test the docs
+    "doc/test_sphinxdocs.py"
   ];
 
   meta = {
-    changelog = "https://github.com/python-control/python-control/releases/tag/${src.tag}";
     description = "Python Control Systems Library";
+    changelog = "https://github.com/python-control/python-control/releases/tag/${src.tag}";
     homepage = "https://github.com/python-control/python-control";
     license = lib.licenses.bsd3;
     maintainers = with lib.maintainers; [ Peter3579 ];
diff --git a/pkgs/development/python-modules/flickrapi/default.nix b/pkgs/development/python-modules/flickrapi/default.nix
index 9bbd11bd65b6..973e1c51827e 100644
--- a/pkgs/development/python-modules/flickrapi/default.nix
+++ b/pkgs/development/python-modules/flickrapi/default.nix
@@ -63,6 +63,7 @@ buildPythonPackage rec {
     "test_walk"
     "test_xmlnode_format"
     "test_xmlnode_format_error"
+    "test_upload"
   ];
 
   pythonImportsCheck = [ "flickrapi" ];
diff --git a/pkgs/development/python-modules/gdsfactory/default.nix b/pkgs/development/python-modules/gdsfactory/default.nix
index b591a368133f..f7aeeb5972a2 100644
--- a/pkgs/development/python-modules/gdsfactory/default.nix
+++ b/pkgs/development/python-modules/gdsfactory/default.nix
@@ -46,14 +46,14 @@
 }:
 buildPythonPackage rec {
   pname = "gdsfactory";
-  version = "9.12.0";
+  version = "9.17.0";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "gdsfactory";
     repo = "gdsfactory";
     tag = "v${version}";
-    hash = "sha256-en976F8BjMK8Ku1QXz4MIxTs+mswVBascmGguPXeEbI=";
+    hash = "sha256-1C7Cva5FZsYLpfF3EZt0RFaWRcYdUdid6Oz9iQHeTqo=";
   };
 
   build-system = [ flit-core ];
diff --git a/pkgs/development/python-modules/keras/default.nix b/pkgs/development/python-modules/keras/default.nix
index 93f8a3a14784..a1aa7438c423 100644
--- a/pkgs/development/python-modules/keras/default.nix
+++ b/pkgs/development/python-modules/keras/default.nix
@@ -214,5 +214,7 @@ buildPythonPackage rec {
     changelog = "https://github.com/keras-team/keras/releases/tag/v${version}";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ GaetanLepage ];
+    # Not yet released for tensorflow >= 2.20.0
+    broken = lib.versionAtLeast tensorflow.version "2.20";
   };
 }
diff --git a/pkgs/development/python-modules/kfactory/default.nix b/pkgs/development/python-modules/kfactory/default.nix
index a164a03d5ccb..1d4bde2fd9fc 100644
--- a/pkgs/development/python-modules/kfactory/default.nix
+++ b/pkgs/development/python-modules/kfactory/default.nix
@@ -10,18 +10,20 @@
   # dependencies
   aenum,
   cachetools,
-  gitpython,
   klayout,
   loguru,
   numpy,
-  pydantic,
+  pydantic-extra-types,
   pydantic-settings,
+  pydantic,
+  pygit2,
+  rapidfuzz,
   rectangle-packer,
   requests,
-  ruamel-yaml,
   ruamel-yaml-string,
+  ruamel-yaml,
   scipy,
-  tomli,
+  semver,
   toolz,
   typer,
 
@@ -31,14 +33,14 @@
 
 buildPythonPackage rec {
   pname = "kfactory";
-  version = "1.12.1";
+  version = "1.14.3";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "gdsfactory";
     repo = "kfactory";
     tag = "v${version}";
-    hash = "sha256-C7ner1jkMCHI8/sRiw82l+THhAIWhwJuZ/ctJ9V76Us=";
+    hash = "sha256-dwJqKl6o2w8fxcNMQAvt5dI1k89yoy/PiIH9eo3JQbA=";
   };
 
   build-system = [
@@ -49,18 +51,20 @@ buildPythonPackage rec {
   dependencies = [
     aenum
     cachetools
-    gitpython
     klayout
     loguru
     numpy
     pydantic
+    pydantic-extra-types
     pydantic-settings
+    pygit2
+    rapidfuzz
     rectangle-packer
     requests
     ruamel-yaml
     ruamel-yaml-string
     scipy
-    tomli
+    semver
     toolz
     typer
   ];
@@ -72,6 +76,8 @@ buildPythonPackage rec {
   disabledTestPaths = [
     # https://github.com/gdsfactory/kfactory/issues/511
     "tests/test_pdk.py"
+    # NameError
+    "tests/test_session.py"
   ];
 
   meta = {
diff --git a/pkgs/development/python-modules/libbs/default.nix b/pkgs/development/python-modules/libbs/default.nix
index b69b2c3ddde6..96eed62a0ebe 100644
--- a/pkgs/development/python-modules/libbs/default.nix
+++ b/pkgs/development/python-modules/libbs/default.nix
@@ -7,6 +7,7 @@
   jfx-bridge,
   networkx,
   platformdirs,
+  ply,
   prompt-toolkit,
   psutil,
   pycparser,
@@ -18,6 +19,15 @@
   writableTmpDirAsHomeHook,
 }:
 
+let
+  # Binary files from https://github.com/binsync/bs-artifacts (only used for testing and only here)
+  binaries = fetchFromGitHub {
+    owner = "binsync";
+    repo = "bs-artifacts";
+    rev = "514c2d6ef1875435c9d137bb5d99b6fc74063817";
+    hash = "sha256-P7+BTJgdC9W8cC/7xQduFYllF+0ds1dSlm59/BFvZ2g=";
+  };
+in
 buildPythonPackage rec {
   pname = "libbs";
   version = "2.15.4";
@@ -38,6 +48,7 @@ buildPythonPackage rec {
     jfx-bridge
     networkx
     platformdirs
+    ply
     prompt-toolkit
     psutil
     pycparser
@@ -51,6 +62,14 @@ buildPythonPackage rec {
     writableTmpDirAsHomeHook
   ];
 
+  # Place test binaries in place
+  preCheck = ''
+    export HOME=$TMPDIR
+    mkdir -p $HOME/bs-artifacts/binaries
+    cp -r ${binaries} $HOME/bs-artifacts/binaries
+    export TEST_BINARIES_DIR=$HOME/bs-artifacts/binaries
+  '';
+
   pythonImportsCheck = [ "libbs" ];
 
   disabledTests = [
diff --git a/pkgs/development/python-modules/mkdocstrings/default.nix b/pkgs/development/python-modules/mkdocstrings/default.nix
index 071370db4f7d..b180498bd6c8 100644
--- a/pkgs/development/python-modules/mkdocstrings/default.nix
+++ b/pkgs/development/python-modules/mkdocstrings/default.nix
@@ -17,14 +17,14 @@
 
 buildPythonPackage rec {
   pname = "mkdocstrings";
-  version = "0.30.0";
+  version = "0.30.1";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "mkdocstrings";
     repo = "mkdocstrings";
     tag = version;
-    hash = "sha256-tJErux/90zXaV0ViGJOQKMf1yYCxMhH1nMrQlXlHw/Y=";
+    hash = "sha256-BfqxL35prq+pvD21w0BOJx/ls8og+LjtGdOAZlHYGVE=";
   };
 
   postPatch = ''
diff --git a/pkgs/development/python-modules/outlines/default.nix b/pkgs/development/python-modules/outlines/default.nix
index e9162d6bf51b..dc5721df96f6 100644
--- a/pkgs/development/python-modules/outlines/default.nix
+++ b/pkgs/development/python-modules/outlines/default.nix
@@ -95,6 +95,11 @@ buildPythonPackage rec {
     tensorflow
   ];
 
+  pytestFlagsArray = [
+    # FutureWarning: functools.partial will be a method descriptor in future Python versions; wrap it in enum.member() if you want to preserve the old behavior
+    "-Wignore::FutureWarning"
+  ];
+
   disabledTests = [
     # Try to dowload models from Hugging Face Hub
     "test_application_callable_call"
diff --git a/pkgs/development/python-modules/parquet/default.nix b/pkgs/development/python-modules/parquet/default.nix
index 5c01bd16752e..fe45aab74aa6 100644
--- a/pkgs/development/python-modules/parquet/default.nix
+++ b/pkgs/development/python-modules/parquet/default.nix
@@ -48,12 +48,17 @@ buildPythonPackage rec {
     "testFromExample"
   ];
 
-  pythonImportsCheck = [ "thriftpy2" ];
+  disabledTestPaths = [
+    # Test is outdated
+    "test/test_read_support.py"
+  ];
+
+  pythonImportsCheck = [ "parquet" ];
 
   meta = with lib; {
     description = "Python implementation of the parquet columnar file format";
     homepage = "https://github.com/jcrobak/parquet-python";
-    changelog = "https://github.com/jcrobak/parquet-python/releases/tag/v${version}";
+    changelog = "https://github.com/jcrobak/parquet-python/releases/tag/${src.tag}";
     license = licenses.bsd2;
     maintainers = with maintainers; [ fab ];
     mainProgram = "parquet";
diff --git a/pkgs/development/python-modules/switchbot-api/default.nix b/pkgs/development/python-modules/switchbot-api/default.nix
index 94812f6f638d..5d2a4daccbf3 100644
--- a/pkgs/development/python-modules/switchbot-api/default.nix
+++ b/pkgs/development/python-modules/switchbot-api/default.nix
@@ -9,7 +9,7 @@
 
 buildPythonPackage rec {
   pname = "switchbot-api";
-  version = "2.7.0";
+  version = "2.8.0";
   pyproject = true;
 
   disabled = pythonOlder "3.10";
@@ -18,7 +18,7 @@ buildPythonPackage rec {
     owner = "SeraphicCorp";
     repo = "py-switchbot-api";
     tag = "v${version}";
-    hash = "sha256-uGaM/pzO9HuLJjXdhdrCfbTxMvYxF4OgFo/m5R2jm5s=";
+    hash = "sha256-xalIVkmzflUVkw/DFOLas6T/jUXSs3gZhEa3IJWtEaw=";
   };
 
   build-system = [ poetry-core ];
diff --git a/pkgs/development/python-modules/tensorflow/binary-hashes.nix b/pkgs/development/python-modules/tensorflow/binary-hashes.nix
index dd536885ace8..023a69666d53 100644
--- a/pkgs/development/python-modules/tensorflow/binary-hashes.nix
+++ b/pkgs/development/python-modules/tensorflow/binary-hashes.nix
@@ -1,72 +1,88 @@
 {
-  version = "2.19.0";
+  version = "2.20.0";
   version_jetson = "2.16.1+nv24.08";
   x86_64-linux_39 = {
-    url = "https://storage.googleapis.com/tensorflow/versions/2.19.0/tensorflow_cpu-2.19.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
-    sha256 = "13xvghhqjlq5l6gnnlkslqyk7iwy2lbhblz70pa0wrsvdiwp9k86";
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow_cpu-2.20.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
+    sha256 = "1nxmm37miz0kzq8g2zc5f9w5vaiz0m75g2q97v19f0pnpl4q1kwh";
   };
   x86_64-linux_310 = {
-    url = "https://storage.googleapis.com/tensorflow/versions/2.19.0/tensorflow_cpu-2.19.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
-    sha256 = "0lgjy7frlh5ax97pc5x2cdq560ybizjrdxms57rcx8r9x8wskrff";
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow_cpu-2.20.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
+    sha256 = "10y5s4bd1s4yk9qx71ap743l8l17axvj5lk49f4fwhq584wg4ghs";
   };
   x86_64-linux_311 = {
-    url = "https://storage.googleapis.com/tensorflow/versions/2.19.0/tensorflow_cpu-2.19.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
-    sha256 = "0l8wgqjhp0srqs4rkij881nxifdzaxkin237wfjqh8h1wdd312ck";
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow_cpu-2.20.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
+    sha256 = "1077zld9n53w72sbvzll2ic1f05liy2jrbfhnlm98vi55nz6nxfg";
   };
   x86_64-linux_312 = {
-    url = "https://storage.googleapis.com/tensorflow/versions/2.19.0/tensorflow_cpu-2.19.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
-    sha256 = "1wxpgzs3d0wblvvg02267j0bw9b8j4dlfspfmp6r8hd6dk9bx78b";
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow_cpu-2.20.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
+    sha256 = "19yn5ligcazva59bgw7v6pdl2wp7xz9i9qf4jpnr9041hm0j5af7";
+  };
+  x86_64-linux_313 = {
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow_cpu-2.20.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
+    sha256 = "1db4gipi9x05r4fbdj98p3bk6pz0zq25xi15c97ch3p1wn8pfvns";
   };
   x86_64-linux_39_gpu = {
-    url = "https://storage.googleapis.com/tensorflow/versions/2.19.0/tensorflow-2.19.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
-    sha256 = "14vgkx1wjf0jiali4lm3x8n6z29m8vdhjva4yvabzc9b1s1757w4";
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow-2.20.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
+    sha256 = "1hwfakj3b5w0lc641bqqcnxhdd47037998aqs57valzw7mc5rsqd";
   };
   x86_64-linux_310_gpu = {
-    url = "https://storage.googleapis.com/tensorflow/versions/2.19.0/tensorflow-2.19.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
-    sha256 = "1s1myi67iqhjxvfvjv8pl26hxjcgya9k1r1hblh8hm0h933xdql3";
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow-2.20.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
+    sha256 = "07jr5bpvmxd3yjw3v2jd9i3jswlsfxr26604r16ka38f04x7zgbs";
   };
   x86_64-linux_311_gpu = {
-    url = "https://storage.googleapis.com/tensorflow/versions/2.19.0/tensorflow-2.19.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
-    sha256 = "1r4ghr51h2bb7dj8q6wydgnvzw0f48b6kkygl6gq0yf9d9w4f1rr";
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow-2.20.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
+    sha256 = "17i2z37jrji8rk11pspmlkd8r297x3an3gj5i7g86ic21zyrj528";
   };
   x86_64-linux_312_gpu = {
-    url = "https://storage.googleapis.com/tensorflow/versions/2.19.0/tensorflow-2.19.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
-    sha256 = "1xm66mwrdxrqs9i68dlahqrd5imgibcz5f3i4ksyg4yp9icjd2z2";
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow-2.20.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
+    sha256 = "1v2jkhglfrh4by86nri7zq4shi2gl920rilw3r5xbq17ql5mn9i5";
+  };
+  x86_64-linux_313_gpu = {
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow-2.20.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl";
+    sha256 = "0wkklfh0ny4y4lzac540v8g745b5adyzp29bi2cmmxr606dp58sz";
   };
   aarch64-linux_39 = {
-    url = "https://storage.googleapis.com/tensorflow/versions/2.19.0/tensorflow-2.19.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl";
-    sha256 = "121amcj78mkkvs2fclc7z669q45x4sa7x6vlzggrm09b0nr7zf4w";
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow-2.20.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl";
+    sha256 = "1pzbi2calx0crx8f0ff1kbibn1j5wwjbvpp9rsmqxja9j9sk7g18";
   };
   aarch64-linux_310 = {
-    url = "https://storage.googleapis.com/tensorflow/versions/2.19.0/tensorflow-2.19.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl";
-    sha256 = "0p4fjsal8kfizcz456lbbqg2i35ljxhdqij7vhsfbvismqy2jf9b";
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow-2.20.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl";
+    sha256 = "1sms3c4mxy892gaa066nx4xa6m28rhigdav6bc9bgj7mjhyjk802";
   };
   aarch64-linux_311 = {
-    url = "https://storage.googleapis.com/tensorflow/versions/2.19.0/tensorflow-2.19.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl";
-    sha256 = "1670dv3kbmxiz4v0ivmkbiiiaa1sbc2x841z6kmy03mcb3wkybf9";
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow-2.20.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl";
+    sha256 = "1mfflmpmywqihd1mdwcq6jnzgsv2khkf68z2dckc01fbxz46i59y";
   };
   aarch64-linux_312 = {
-    url = "https://storage.googleapis.com/tensorflow/versions/2.19.0/tensorflow-2.19.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl";
-    sha256 = "020kppmgmv4hnz3dqmam01gq95s69xjn6zn6k25l08zf6fyvzx0h";
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow-2.20.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl";
+    sha256 = "13q71s5gjb405s48maqz4sckwx971lwj5sg1bz2gyaz2s0yzpyrb";
+  };
+  aarch64-linux_313 = {
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow-2.20.0-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl";
+    sha256 = "09nrnffmqdfr9zy5l1li0727b02drlz4p2dlfx4ss7kzl02qxj27";
   };
   aarch64-linux_310_jetson = {
     url = "https://developer.download.nvidia.com/compute/redist/jp/v61/tensorflow/tensorflow-2.16.1+nv24.08-cp310-cp310-linux_aarch64.whl";
     sha256 = "0z18zdcjc2dingl94kivhd5cpzbvkjp9j12q57acjppp4hyd6g7f";
   };
   aarch64-darwin_39 = {
-    url = "https://storage.googleapis.com/tensorflow/versions/2.19.0/tensorflow-2.19.0-cp39-cp39-macosx_12_0_arm64.whl";
-    sha256 = "02fb702d2wmdgrjq8jj46bp51sh1l9j4q9z231x151z2i3sdn5dd";
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow-2.20.0-cp39-cp39-macosx_12_0_arm64.whl";
+    sha256 = "0g3qg53l8pfna5r964s08das8jsijbg81snb8ny3z79034dvsv56";
   };
   aarch64-darwin_310 = {
-    url = "https://storage.googleapis.com/tensorflow/versions/2.19.0/tensorflow-2.19.0-cp310-cp310-macosx_12_0_arm64.whl";
-    sha256 = "0d6anjqkm5vq22awxhcwivjdshnlzmby80by3icyjcihbkr08mn9";
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow-2.20.0-cp310-cp310-macosx_12_0_arm64.whl";
+    sha256 = "0msk3aw06q46n4ng8i5cs79r6bhmmvqcam78pdav42hkypw6kwg5";
   };
   aarch64-darwin_311 = {
-    url = "https://storage.googleapis.com/tensorflow/versions/2.19.0/tensorflow-2.19.0-cp311-cp311-macosx_12_0_arm64.whl";
-    sha256 = "05f12garj6ad4vcxxpi0vihps4gh9y30bffp2qy1k36qi8kn5m38";
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow-2.20.0-cp311-cp311-macosx_12_0_arm64.whl";
+    sha256 = "1visqvq280k4cgmg6hwphfkq54p8kdrnnsi4baw0jp83qlb415jz";
   };
   aarch64-darwin_312 = {
-    url = "https://storage.googleapis.com/tensorflow/versions/2.19.0/tensorflow-2.19.0-cp312-cp312-macosx_12_0_arm64.whl";
-    sha256 = "1bibid6mrgmjra291pmb7b5sf49f8jpi3n8x8mdwjhfmxfz1c6c2";
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow-2.20.0-cp312-cp312-macosx_12_0_arm64.whl";
+    sha256 = "13vcl3wcgaid8f2rdzvzmkfbdl3hhkh7qlwdy88apmrg4gq25caj";
+  };
+  aarch64-darwin_313 = {
+    url = "https://storage.googleapis.com/tensorflow/versions/2.20.0/tensorflow-2.20.0-cp313-cp313-macosx_12_0_arm64.whl";
+    sha256 = "19g8kk7f7ylx1y7awpc3afw7hp50sid2ka0jd9fdmh1q7dhhnzqr";
   };
 }
diff --git a/pkgs/development/python-modules/tensorflow/default.nix b/pkgs/development/python-modules/tensorflow/default.nix
index 5e6fe4326ff5..85055efe84e3 100644
--- a/pkgs/development/python-modules/tensorflow/default.nix
+++ b/pkgs/development/python-modules/tensorflow/default.nix
@@ -605,7 +605,7 @@ in
 buildPythonPackage {
   __structuredAttrs = true;
   inherit version pname format;
-  disabled = pythonAtLeast "3.12";
+  disabled = pythonAtLeast "3.13";
 
   src = bazel-build.python;
 
@@ -613,7 +613,7 @@ buildPythonPackage {
   # - Drop tensorflow-io dependency until we get it to build
   # - Relax flatbuffers and gast version requirements
   # - The purpose of python3Packages.libclang is not clear at the moment and we don't have it packaged yet
-  # - keras and tensorlow-io-gcs-filesystem will be considered as optional for now.
+  # - keras will be considered as optional for now.
   postPatch = ''
     sed -i setup.py \
       -e '/tensorflow-io-gcs-filesystem/,+1d' \
@@ -621,7 +621,6 @@ buildPythonPackage {
       -e "s/'gast[^']*',/'gast',/" \
       -e "/'libclang[^']*',/d" \
       -e "/'keras[^']*')\?,/d" \
-      -e "/'tensorflow-io-gcs-filesystem[^']*',/d" \
       -e "s/'protobuf[^']*',/'protobuf',/" \
   '';
 
diff --git a/pkgs/development/python-modules/tensorflow/prefetcher.sh b/pkgs/development/python-modules/tensorflow/prefetcher.sh
index 9bdf9bf3930e..c80ed6fe646c 100755
--- a/pkgs/development/python-modules/tensorflow/prefetcher.sh
+++ b/pkgs/development/python-modules/tensorflow/prefetcher.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-version="2.19.0"
+version="2.20.0"
 version_jetson="2.16.1+nv24.08"
 
 bucket="https://storage.googleapis.com/tensorflow/versions/${version}"
@@ -8,25 +8,29 @@ bucket_jetson="https://developer.download.nvidia.com/compute/redist/jp/v61/tenso
 
 # List of binary wheels for Tensorflow.  The most recent versions can be found
 # on the following page:
-# https://www.tensorflow.org/install/pip?lang=python3#package-location
+# https://www.tensorflow.org/install/pip?lang=python3#package_location
 url_and_key_list=(
 "x86_64-linux_39 $bucket/tensorflow_cpu-${version}-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"
 "x86_64-linux_310 $bucket/tensorflow_cpu-${version}-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"
 "x86_64-linux_311 $bucket/tensorflow_cpu-${version}-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"
 "x86_64-linux_312 $bucket/tensorflow_cpu-${version}-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"
+"x86_64-linux_313 $bucket/tensorflow_cpu-${version}-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"
 "x86_64-linux_39_gpu $bucket/tensorflow-${version}-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"
 "x86_64-linux_310_gpu $bucket/tensorflow-${version}-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"
 "x86_64-linux_311_gpu $bucket/tensorflow-${version}-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"
 "x86_64-linux_312_gpu $bucket/tensorflow-${version}-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"
+"x86_64-linux_313_gpu $bucket/tensorflow-${version}-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl"
 "aarch64-linux_39 $bucket/tensorflow-${version}-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl"
 "aarch64-linux_310 $bucket/tensorflow-${version}-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl"
 "aarch64-linux_311 $bucket/tensorflow-${version}-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl"
 "aarch64-linux_312 $bucket/tensorflow-${version}-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl"
+"aarch64-linux_313 $bucket/tensorflow-${version}-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl"
 "aarch64-linux_310_jetson $bucket_jetson/tensorflow-${version_jetson}-cp310-cp310-linux_aarch64.whl"
 "aarch64-darwin_39 $bucket/tensorflow-${version}-cp39-cp39-macosx_12_0_arm64.whl"
 "aarch64-darwin_310 $bucket/tensorflow-${version}-cp310-cp310-macosx_12_0_arm64.whl"
 "aarch64-darwin_311 $bucket/tensorflow-${version}-cp311-cp311-macosx_12_0_arm64.whl"
 "aarch64-darwin_312 $bucket/tensorflow-${version}-cp312-cp312-macosx_12_0_arm64.whl"
+"aarch64-darwin_313 $bucket/tensorflow-${version}-cp313-cp313-macosx_12_0_arm64.whl"
 )
 
 hashfile=binary-hashes.nix
diff --git a/pkgs/development/python-modules/tf-keras/default.nix b/pkgs/development/python-modules/tf-keras/default.nix
index 4643ea82ef4c..e4dbdc919934 100644
--- a/pkgs/development/python-modules/tf-keras/default.nix
+++ b/pkgs/development/python-modules/tf-keras/default.nix
@@ -18,13 +18,13 @@
 
 buildPythonPackage rec {
   pname = "tf-keras";
-  version = "2.19.0";
+  version = "2.20.1";
   pyproject = true;
 
   src = fetchPypi {
     pname = "tf_keras";
     inherit version;
-    hash = "sha256-sJpAfYekVxzh6MqYXPxoSD49Y7JRil15qXrZLLZNvpw=";
+    hash = "sha256-iEvlk4+wsrU7FYPBritmDvhyFTd8KbW2p3/SIbRyrq8=";
   };
 
   build-system = [
diff --git a/pkgs/development/python-modules/tree-sitter-sql/default.nix b/pkgs/development/python-modules/tree-sitter-sql/default.nix
index d5df98fa4906..91d83cdd43fb 100644
--- a/pkgs/development/python-modules/tree-sitter-sql/default.nix
+++ b/pkgs/development/python-modules/tree-sitter-sql/default.nix
@@ -12,14 +12,14 @@
 }:
 buildPythonPackage rec {
   pname = "tree-sitter-sql";
-  version = "0.3.8";
+  version = "0.3.10";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "DerekStride";
     repo = "tree-sitter-sql";
     tag = "v${version}";
-    hash = "sha256-8gdbbz187sV8I+PJHubFyyQwGUqvo05Yw1DX7rOK4DI=";
+    hash = "sha256-vPPlDdLkenLG8uH26fzMOS3oxClCLSIKa6zhmDbnC/A=";
   };
 
   postUnpack = ''
@@ -53,6 +53,7 @@ buildPythonPackage rec {
   meta = {
     description = "Sql grammar for tree-sitter";
     homepage = "https://github.com/DerekStride/tree-sitter-sql";
+    changelog = "https://github.com/DerekStride/tree-sitter-sql/releases/tag/${src.tag}";
     license = lib.licenses.mit;
     maintainers = with lib.maintainers; [ pcboy ];
   };
diff --git a/pkgs/development/python-modules/types-lxml/default.nix b/pkgs/development/python-modules/types-lxml/default.nix
index 02e93cd4cd46..dc497d82fe53 100644
--- a/pkgs/development/python-modules/types-lxml/default.nix
+++ b/pkgs/development/python-modules/types-lxml/default.nix
@@ -73,6 +73,11 @@ buildPythonPackage rec {
   disabledTests = [
     "test_single_ns_all_tag_2"
     "test_default_ns"
+    # Tests require network access
+    "TestRelaxNGInput"
+    "TestXmldtdid"
+    "TestIddict"
+    "TestParseid"
   ];
 
   meta = with lib; {
diff --git a/pkgs/development/python-modules/types-regex/default.nix b/pkgs/development/python-modules/types-regex/default.nix
index 5925a5b27e56..669d7361fca4 100644
--- a/pkgs/development/python-modules/types-regex/default.nix
+++ b/pkgs/development/python-modules/types-regex/default.nix
@@ -7,13 +7,13 @@
 
 buildPythonPackage rec {
   pname = "types-regex";
-  version = "2025.9.1.20250903";
+  version = "2025.9.18.20250921";
   pyproject = true;
 
   src = fetchPypi {
     pname = "types_regex";
     inherit version;
-    hash = "sha256-IwEW9ktcCLBhCdlQCG5V/ICbiipdE+gCGKx880+arIQ=";
+    hash = "sha256-4XAMIbHDEpDkpt1iWE7R8dadcE7RZ2toqO2i0dJCDD8=";
   };
 
   build-system = [
diff --git a/pkgs/tools/misc/qmake2cmake/default.nix b/pkgs/tools/misc/qmake2cmake/default.nix
index 1d2e6c49d487..99d9a8120c94 100644
--- a/pkgs/tools/misc/qmake2cmake/default.nix
+++ b/pkgs/tools/misc/qmake2cmake/default.nix
@@ -6,26 +6,30 @@
   platformdirs,
   portalocker,
   pyparsing,
+  setuptools,
   sympy,
   pytestCheckHook,
+  writableTmpDirAsHomeHook,
 }:
 
 buildPythonPackage rec {
   pname = "qmake2cmake";
-  version = "1.0.6";
-  format = "setuptools";
+  version = "1.0.7";
+  pyproject = true;
 
   src = fetchgit {
     url = "https://codereview.qt-project.org/qt/qmake2cmake";
-    rev = "v${version}";
-    hash = "sha256-M5XVQ8MXo2Yxg5eZCho2YAGFtB0h++mEAg8NcQVuP/w=";
+    tag = "v${version}";
+    hash = "sha256-Y1HU4bNZY0b1C8HIX43AR24zoIyTEgkVXpnweEBlOYk=";
   };
 
   patches = [
     ./fix-locations.patch
   ];
 
-  propagatedBuildInputs = [
+  build-system = [ setuptools ];
+
+  dependencies = [
     packaging
     platformdirs
     portalocker
@@ -35,16 +39,13 @@ buildPythonPackage rec {
 
   nativeCheckInputs = [
     pytestCheckHook
+    writableTmpDirAsHomeHook
   ];
 
-  preCheck = ''
-    export HOME=$(mktemp -d)
-  '';
-
-  meta = with lib; {
+  meta = {
     description = "Tool to convert qmake .pro files to CMakeLists.txt";
     homepage = "https://wiki.qt.io/Qmake2cmake";
-    license = licenses.gpl3Plus;
-    maintainers = with maintainers; [ wegank ];
+    license = lib.licenses.gpl3Plus;
+    maintainers = with lib.maintainers; [ wegank ];
   };
 }
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index fd4f2818b78b..b6af550d204c 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -1202,6 +1202,7 @@ mapAliases {
   ipfs-migrator-unwrapped = kubo-migrator-unwrapped; # Added 2022-09-27
   ipfs-migrator = kubo-migrator; # Added 2022-09-27
   iproute = throw "'iproute' has been renamed to/replaced by 'iproute2'"; # Converted to throw 2024-10-17
+  ir.lv2 = ir-lv2; # Added 2025-09-37
   irrlichtmt = throw "irrlichtmt has been removed because it was moved into the Minetest repo"; # Added 2024-08-12
   isl_0_11 = throw "isl_0_11 has been removed from Nixpkgs, as it is unmaintained and obsolete"; # Added 2024-09-13
   isl_0_14 = throw "isl_0_14 has been removed from Nixpkgs, as it is unmaintained and obsolete"; # Added 2024-09-13
@@ -1224,6 +1225,7 @@ mapAliases {
   jd-cli = throw "jd-cli has been removed due to upstream being unmaintained since 2019. Other Java decompilers in Nixpkgs include bytecode-viewer (GUI), cfr (CLI), and procyon (CLI)."; # Added 2024-10-30
   jd-gui = throw "jd-gui has been removed due to a dependency on the dead JCenter Bintray. Other Java decompilers in Nixpkgs include bytecode-viewer (GUI), cfr (CLI), and procyon (CLI)."; # Added 2024-10-30
   jikespg = throw "'jikespg' has been removed due to lack of maintenance upstream."; # Added 2025-06-10
+  jing = jing-trang; # Added 2025-09-18
   jsawk = throw "'jsawk' has been removed because it is unmaintained upstream"; # Added 2024-08-07
   jscoverage = throw "jscoverage has been removed, as it was broken"; # Added 2025-08-25
 
@@ -1608,6 +1610,7 @@ mapAliases {
   mailcore2 = throw "'mailcore2' has been removed due to lack of upstream maintenance."; # Added 2025-06-09
   mailctl = throw "mailctl has been renamed to oama"; # Added 2024-08-19
   mailman-rss = throw "The mailman-rss package was dropped since it was unmaintained."; # Added 2024-06-21
+  melmatcheq.lv2 = melmatcheq-lv2; # Added 2025-09-27
   mariadb_105 = throw "'mariadb_105' has been removed because it reached its End of Life. Consider upgrading to 'mariadb_106'."; # Added 2025-04-26
   mariadb_110 = throw "mariadb_110 has been removed from nixpkgs, please switch to another version like mariadb_114"; # Added 2024-08-15
   mariadb-client = hiPrio mariadb.client; # added 2019.07.28
@@ -2437,6 +2440,7 @@ mapAliases {
   tabula = throw "tabula has been removed from nixpkgs, as it was broken"; # Added 2024-07-15
   tailor = throw "'tailor' has been removed from nixpkgs, as it was unmaintained upstream."; # Added 2024-11-02
   tangogps = throw "'tangogps' has been renamed to/replaced by 'foxtrotgps'"; # Converted to throw 2024-10-17
+  tamgamp.lv2 = tamgamp-lv2; # Added 2025-09-27
   taskwarrior = lib.warnOnInstantiate "taskwarrior was replaced by taskwarrior3, which requires manual transition from taskwarrior 2.6, read upstream's docs: https://taskwarrior.org/docs/upgrade-3/" taskwarrior2; # Added 2024-08-14
   taplo-cli = taplo; # Added 2022-07-30
   taplo-lsp = taplo; # Added 2022-07-30
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 2987543aade1..0d1f95e52dd5 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -1083,12 +1083,6 @@ with pkgs;
 
   makehuman = libsForQt5.callPackage ../applications/misc/makehuman { };
 
-  mcaselector = callPackage ../tools/games/minecraft/mcaselector {
-    jre = jre.override {
-      enableJavaFX = true;
-    };
-  };
-
   mkosi = callPackage ../tools/virtualization/mkosi { };
 
   mkosi-full = mkosi.override { withQemu = true; };
@@ -1118,10 +1112,6 @@ with pkgs;
 
   shaperglot = with python3Packages; toPythonApplication shaperglot;
 
-  slipstream = callPackage ../tools/games/slipstream {
-    jdk = jdk8;
-  };
-
   supermin = callPackage ../tools/virtualization/supermin {
     ocamlPackages = ocaml-ng.ocamlPackages_4_14;
   };
@@ -1687,14 +1677,6 @@ with pkgs;
 
   guglielmo = libsForQt5.callPackage ../applications/radio/guglielmo { };
 
-  gremlin-console = callPackage ../applications/misc/gremlin-console {
-    openjdk = openjdk11;
-  };
-
-  gremlin-server = callPackage ../applications/misc/gremlin-server {
-    openjdk = openjdk11;
-  };
-
   hinit = haskell.lib.compose.justStaticExecutables haskellPackages.hinit;
 
   hwi = with python3Packages; toPythonApplication hwi;
@@ -3213,11 +3195,6 @@ with pkgs;
 
   jello = with python3Packages; toPythonApplication jello;
 
-  jing = res.jing-trang;
-  jing-trang = callPackage ../tools/text/xml/jing-trang {
-    jdk_headless = jdk8_headless; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
-  };
-
   jl = haskellPackages.jl;
 
   joplin = nodePackages.joplin;
@@ -3265,10 +3242,6 @@ with pkgs;
 
   keybase-gui = callPackage ../tools/security/keybase/gui.nix { };
 
-  keystore-explorer = callPackage ../applications/misc/keystore-explorer {
-    jdk = jdk11;
-  };
-
   kio-fuse = libsForQt5.callPackage ../tools/filesystems/kio-fuse { };
 
   krunvm = callPackage ../applications/virtualization/krunvm {
@@ -3707,10 +3680,6 @@ with pkgs;
 
   onlykey = callPackage ../tools/security/onlykey { };
 
-  openapi-generator-cli = callPackage ../tools/networking/openapi-generator-cli {
-    jre = pkgs.jre_headless;
-  };
-
   ophcrack-cli = ophcrack.override { enableGui = false; };
 
   open-interpreter = with python3Packages; toPythonApplication open-interpreter;
@@ -3730,8 +3699,6 @@ with pkgs;
     privsepPath = "/var/empty";
   };
 
-  openrefine = callPackage ../applications/science/misc/openrefine { jdk = jdk17; };
-
   openrgb-with-all-plugins = openrgb.withPlugins [
     openrgb-plugin-effects
     openrgb-plugin-hardwaresync
@@ -4125,10 +4092,6 @@ with pkgs;
     pulseaudioSupport = config.pulseaudio or stdenv.hostPlatform.isLinux;
   };
 
-  soapui = callPackage ../applications/networking/soapui {
-    jdk = jdk11;
-  };
-
   specup = haskellPackages.specup.bin;
 
   spglib = callPackage ../development/libraries/spglib {
@@ -4567,18 +4530,10 @@ with pkgs;
   adaptivecppWithCuda = adaptivecpp.override { cudaSupport = true; };
   adaptivecppWithRocm = adaptivecpp.override { rocmSupport = true; };
 
-  adoptopenjdk-icedtea-web = callPackage ../development/compilers/adoptopenjdk-icedtea-web {
-    jdk = jdk8;
-  };
-
   armips = callPackage ../by-name/ar/armips/package.nix {
     stdenv = clangStdenv;
   };
 
-  ballerina = callPackage ../development/compilers/ballerina {
-    openjdk = openjdk17_headless;
-  };
-
   binaryen = callPackage ../development/compilers/binaryen {
     nodejs = nodejs-slim;
     inherit (python3Packages) filecheck;
@@ -5581,9 +5536,6 @@ with pkgs;
     coursier = coursier.override { jre = jdk8; };
   };
 
-  scalafix = callPackage ../development/tools/scalafix {
-    jre = jre8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
-  };
   # smlnjBootstrap should be redundant, now that smlnj works on Darwin natively
   smlnjBootstrap = callPackage ../development/compilers/smlnj/bootstrap.nix { };
   smlnj = callPackage ../development/compilers/smlnj { };
@@ -5826,10 +5778,7 @@ with pkgs;
     xeus-cling
     ;
 
-  clojure = callPackage ../development/interpreters/clojure {
-    # set this to an LTS version of java
-    jdk = jdk21;
-  };
+  clojure = callPackage ../development/interpreters/clojure { };
 
   clooj = callPackage ../development/interpreters/clojure/clooj.nix { };
 
@@ -5920,11 +5869,6 @@ with pkgs;
 
   jpm = callPackage ../development/interpreters/janet/jpm.nix { };
 
-  davmail = callPackage ../applications/networking/davmail {
-    jre = jdk11.override { enableJavaFX = true; };
-    zulu = zulu11.override { enableJavaFX = true; };
-  };
-
   lambda-lisp-blc = lambda-lisp;
 
   love_0_10 = callPackage ../development/interpreters/love/0.10.nix { };
@@ -6805,13 +6749,6 @@ with pkgs;
     inochi-session
     ;
 
-  javacc = callPackage ../development/tools/parsing/javacc {
-    # Upstream doesn't support anything newer than Java 8.
-    # https://github.com/javacc/javacc/blob/c708628423b71ce8bc3b70143fa5b6a2b7362b3a/README.md#building-javacc-from-source
-    jdk = jdk8;
-    jre = jre8;
-  };
-
   jenkins-job-builder = with python3Packages; toPythonApplication jenkins-job-builder;
 
   kustomize = callPackage ../development/tools/kustomize { };
@@ -7108,10 +7045,6 @@ with pkgs;
 
   gdbHostCpuOnly = gdb.override { hostCpuOnly = true; };
 
-  jprofiler = callPackage ../development/tools/java/jprofiler {
-    jdk = jdk11;
-  };
-
   valgrind-light = (valgrind.override { gdb = null; }).overrideAttrs (oldAttrs: {
     meta = oldAttrs.meta // {
       description = "${oldAttrs.meta.description} (without GDB)";
@@ -7147,10 +7080,6 @@ with pkgs;
 
   xxdiff-tip = xxdiff;
 
-  yourkit-java = callPackage ../by-name/yo/yourkit-java/package.nix {
-    jre = jdk21;
-  };
-
   yq = python3.pkgs.toPythonApplication python3.pkgs.yq;
 
   mypy = with python3Packages; toPythonApplication mypy;
@@ -8130,10 +8059,6 @@ with pkgs;
 
   malcontent-ui = callPackage ../development/libraries/malcontent/ui.nix { };
 
-  libmatthew_java = callPackage ../development/libraries/java/libmatthew-java {
-    jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
-  };
-
   inherit
     ({
       libmicrohttpd_0_9_77 = callPackage ../development/libraries/libmicrohttpd/0.9.77.nix { };
@@ -9137,10 +9062,6 @@ with pkgs;
 
   ### DEVELOPMENT / LIBRARIES / JAVA
 
-  javaCup = callPackage ../development/libraries/java/cup {
-    jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
-  };
-
   saxonb = saxonb_8_8;
   saxon-he = saxon_12-he;
 
@@ -9213,11 +9134,7 @@ with pkgs;
 
   # Armed Bear Common Lisp
   abcl = wrapLisp {
-    pkg = callPackage ../development/compilers/abcl {
-      # https://armedbear.common-lisp.dev/ lists OpenJDK 17 as the highest
-      # supported JDK.
-      jdk = openjdk17;
-    };
+    pkg = callPackage ../development/compilers/abcl { };
     faslExt = "abcl";
   };
 
@@ -9537,10 +9454,6 @@ with pkgs;
 
   dodgy = with python3Packages; toPythonApplication dodgy;
 
-  envoy = callPackage ../by-name/en/envoy/package.nix {
-    jdk = openjdk11_headless;
-  };
-
   etcd = etcd_3_5;
   etcd_3_4 = callPackage ../servers/etcd/3_4 { };
   etcd_3_5 = callPackage ../servers/etcd/3_5 { };
@@ -9550,11 +9463,6 @@ with pkgs;
     withExtraLuaPackages = _: [ ];
   };
 
-  elasticmq-server-bin = callPackage ../servers/elasticmq-server-bin {
-    jre = jre8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
-    jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
-  };
-
   felix = callPackage ../servers/felix { };
 
   felix_remoteshell = callPackage ../servers/felix/remoteshell.nix { };
@@ -11313,13 +11221,6 @@ with pkgs;
 
   espeakedit = callPackage ../applications/audio/espeak/edit.nix { };
 
-  greenfoot = callPackage ../applications/editors/greenfoot {
-    openjdk = openjdk21.override {
-      enableJavaFX = true;
-      openjfx_jdk = openjfx21.override { withWebKit = true; };
-    };
-  };
-
   input-leap = qt6Packages.callPackage ../applications/misc/input-leap {
     avahi = avahi.override { withLibdnssdCompat = true; };
   };
@@ -11359,12 +11260,6 @@ with pkgs;
 
   fvwm = fvwm2;
 
-  ganttproject-bin = callPackage ../applications/misc/ganttproject-bin {
-    jre = openjdk17.override {
-      enableJavaFX = true;
-    };
-  };
-
   gaucheBootstrap = callPackage ../development/interpreters/gauche/boot.nix { };
 
   gauche = callPackage ../development/interpreters/gauche { };
@@ -11624,10 +11519,6 @@ with pkgs;
 
   molsketch = libsForQt5.callPackage ../applications/editors/molsketch { };
 
-  pattypan = callPackage ../applications/misc/pattypan {
-    jdk = jdk.override { enableJavaFX = true; };
-  };
-
   gphoto2 = callPackage ../applications/misc/gphoto2 { };
 
   gphoto2fs = callPackage ../applications/misc/gphoto2/gphotofs.nix { };
@@ -11896,8 +11787,6 @@ with pkgs;
     lua = lua5_1;
   };
 
-  ir.lv2 = callPackage ../applications/audio/ir.lv2 { };
-
   jabcode = callPackage ../development/libraries/jabcode { };
 
   jabcode-writer = callPackage ../development/libraries/jabcode {
@@ -11908,13 +11797,6 @@ with pkgs;
     subproject = "reader";
   };
 
-  jabref = callPackage ../applications/office/jabref {
-    jdk = jdk21.override {
-      enableJavaFX = true;
-      openjfx_jdk = openjfx23;
-    };
-  };
-
   jackmix = libsForQt5.callPackage ../applications/audio/jackmix { };
   jackmix_jack1 = jackmix.override { jack = jack1; };
 
@@ -12133,8 +12015,6 @@ with pkgs;
   mediaelch-qt5 = callPackage ../by-name/me/mediaelch/package.nix { qtVersion = 5; };
   mediaelch-qt6 = mediaelch;
 
-  melmatcheq.lv2 = callPackage ../applications/audio/melmatcheq.lv2 { };
-
   mendeley = libsForQt5.callPackage ../applications/office/mendeley {
     gconf = gnome2.GConf;
   };
@@ -12525,10 +12405,6 @@ with pkgs;
     imlib2 = imlib2Full;
   };
 
-  processing = callPackage ../applications/graphics/processing {
-    jdk = jdk17;
-  };
-
   # perhaps there are better apps for this task? It's how I had configured my previous system.
   # And I don't want to rewrite all rules
   profanity = callPackage ../applications/networking/instant-messengers/profanity (
@@ -12927,8 +12803,6 @@ with pkgs;
 
   tagainijisho = libsForQt5.callPackage ../applications/office/tagainijisho { };
 
-  tamgamp.lv2 = callPackage ../applications/audio/tamgamp.lv2 { };
-
   telegram-desktop =
     kdePackages.callPackage ../applications/networking/instant-messengers/telegram/telegram-desktop
       {
@@ -14240,18 +14114,6 @@ with pkgs;
 
   raxml-mpi = raxml.override { useMpi = true; };
 
-  trimmomatic = callPackage ../applications/science/biology/trimmomatic {
-    jdk = pkgs.jdk21_headless;
-    # Reduce closure size
-    jre = pkgs.jre_minimal.override {
-      modules = [
-        "java.base"
-        "java.logging"
-      ];
-      jdk = pkgs.jdk21_headless;
-    };
-  };
-
   ### SCIENCE/MACHINE LEARNING
 
   streamlit = with python3Packages; toPythonApplication streamlit;
@@ -14969,10 +14831,6 @@ with pkgs;
     }
   );
 
-  DisnixWebService = callPackage ../tools/package-management/disnix/DisnixWebService {
-    jdk = jdk8;
-  };
-
   lice = python3Packages.callPackage ../tools/misc/lice { };
 
   mysql-workbench = callPackage ../by-name/my/mysql-workbench/package.nix (