treewide: move to by-name part 3

pkgs/by-name/hc/hci/package.nix

@@ -58,6 +58,6 @@ in
 pkg
 // {
   meta = pkg.meta // {
-    position = toString ./default.nix + ":1";
+    position = toString ./package.nix + ":1";
   };
 }

pkgs/by-name/he/hercules-ci-agent/package.nix

@@ -41,7 +41,7 @@ in
 pkg.overrideAttrs (
   finalAttrs: o: {
     meta = o.meta // {
-      position = toString ./default.nix + ":1";
+      position = toString ./package.nix + ":1";
     };
     passthru = o.passthru // {
       tests = {

pkgs/by-name/jm/jmol/package.nix

@@ -4,7 +4,7 @@
   fetchurl,
   unzip,
   makeDesktopItem,
-  jre,
+  jre8,
 }:
 
 let
@@ -44,7 +44,7 @@ stdenv.mkDerivation rec {
     };
 
   patchPhase = ''
-    sed -i -e "4s:.*:command=${jre}/bin/java:" -e "10s:.*:jarpath=$out/share/jmol/Jmol.jar:" -e "11,21d" jmol
+    sed -i -e "4s:.*:command=${jre8}/bin/java:" -e "10s:.*:jarpath=$out/share/jmol/Jmol.jar:" -e "11,21d" jmol
   '';
 
   installPhase = ''

pkgs/top-level/all-packages.nix

@@ -806,8 +806,6 @@ with pkgs;
 
   closureInfo = callPackage ../build-support/closure-info.nix { };
 
-  serverspec = callPackage ../tools/misc/serverspec { };
-
   setupSystemdUnits = callPackage ../build-support/setup-systemd-units.nix { };
 
   shortenPerlShebang = makeSetupHook {
@@ -2710,8 +2708,6 @@ with pkgs;
 
   cve-bin-tool = python3Packages.callPackage ../tools/security/cve-bin-tool { };
 
-  danger-gitlab = callPackage ../applications/version-management/danger-gitlab { };
-
   dconf2nix = callPackage ../development/tools/haskell/dconf2nix { };
 
   ddcui = libsForQt5.callPackage ../applications/misc/ddcui { };
@@ -2746,8 +2742,6 @@ with pkgs;
     dub-to-nix
     ;
 
-  duff = callPackage ../tools/filesystems/duff { };
-
   dvtm = callPackage ../tools/misc/dvtm {
     # if you prefer a custom config, write the config.h in dvtm.config.h
     # and enable
@@ -2756,8 +2750,6 @@ with pkgs;
 
   dvtm-unstable = callPackage ../tools/misc/dvtm/unstable.nix { };
 
-  eid-mw = callPackage ../tools/security/eid-mw { };
-
   engauge-digitizer = libsForQt5.callPackage ../applications/science/math/engauge-digitizer { };
 
   kramdown-asciidoc = callPackage ../tools/typesetting/kramdown-asciidoc { };
@@ -2765,14 +2757,6 @@ with pkgs;
   rocmPackages = rocmPackages_6;
   rocmPackages_6 = recurseIntoAttrs (callPackage ../development/rocm-modules/6 { });
 
-  sonobuoy = callPackage ../applications/networking/cluster/sonobuoy { };
-
-  schleuder = callPackage ../tools/security/schleuder { };
-
-  schleuder-cli = callPackage ../tools/security/schleuder/cli { };
-
-  teamocil = callPackage ../tools/misc/teamocil { };
-
   tsm-client-withGui = callPackage ../by-name/ts/tsm-client/package.nix { enableGui = true; };
 
   tracy = callPackage ../by-name/tr/tracy/package.nix { withWayland = stdenv.hostPlatform.isLinux; };
@@ -4000,8 +3984,6 @@ with pkgs;
 
   pinentry_mac = callPackage ../tools/security/pinentry/mac.nix { };
 
-  pinnwand = callPackage ../servers/pinnwand { };
-
   plan9port = callPackage ../tools/system/plan9port {
     inherit (darwin) DarwinTools;
   };
@@ -4152,8 +4134,6 @@ with pkgs;
 
   recoll-nox = recoll.override { withGui = false; };
 
-  reckon = callPackage ../tools/text/reckon { };
-
   remote-exec = python3Packages.callPackage ../tools/misc/remote-exec { };
 
   reptor = with python3.pkgs; toPythonApplication reptor;
@@ -4166,16 +4146,10 @@ with pkgs;
 
   reuse = with python3.pkgs; toPythonApplication reuse;
 
-  riemann-tools = callPackage ../tools/misc/riemann-tools { };
-
   rmlint = callPackage ../tools/misc/rmlint {
     inherit (python3Packages) sphinx;
   };
 
-  rosenpass = callPackage ../tools/networking/rosenpass { };
-
-  rosenpass-tools = callPackage ../tools/networking/rosenpass/tools.nix { };
-
   rpm = callPackage ../tools/package-management/rpm {
     lua = lua5_4;
   };
@@ -4260,8 +4234,6 @@ with pkgs;
 
   soundkonverter = libsForQt5.soundkonverter;
 
-  steck = callPackage ../servers/pinnwand/steck.nix { };
-
   stm32loader = with python3Packages; toPythonApplication stm32loader;
 
   solc-select = with python3Packages; toPythonApplication solc-select;
@@ -4574,7 +4546,6 @@ with pkgs;
   # It is also needed to reduce the amount of unnecessary stuff in the Darwin bootstrap.
   xarMinimal = callPackage ../by-name/xa/xar/package.nix { e2fsprogs = null; };
 
-  xdelta = callPackage ../tools/compression/xdelta { };
   xdeltaUnstable = callPackage ../tools/compression/xdelta/unstable.nix { };
 
   xdot = with python3Packages; toPythonApplication xdot;
@@ -4629,9 +4600,6 @@ with pkgs;
     nvidiaSupport = true;
   };
 
-  zpaq = callPackage ../tools/archivers/zpaq { };
-  zpaqd = callPackage ../tools/archivers/zpaq/zpaqd.nix { };
-
   zstd = callPackage ../tools/compression/zstd {
     cmake = buildPackages.cmakeMinimal;
   };
@@ -6893,8 +6861,6 @@ with pkgs;
 
   bdep = callPackage ../development/tools/build-managers/build2/bdep.nix { };
 
-  bore-cli = callPackage ../tools/networking/bore-cli/default.nix { };
-
   bpkg = callPackage ../development/tools/build-managers/build2/bpkg.nix { };
 
   buildkite-test-collector-rust =
@@ -6969,8 +6935,6 @@ with pkgs;
 
   cookiecutter = with python3Packages; toPythonApplication cookiecutter;
 
-  corundum = callPackage ../development/tools/corundum { };
-
   ctags = callPackage ../development/tools/misc/ctags { };
 
   ctagsWrapped = callPackage ../development/tools/misc/ctags/wrapped.nix { };
@@ -7322,8 +7286,6 @@ with pkgs;
 
   portableService = callPackage ../build-support/portable-service { };
 
-  polar = callPackage ../tools/misc/polar { };
-
   pyprof2calltree = with python3Packages; toPythonApplication pyprof2calltree;
 
   premake4 = callPackage ../development/tools/misc/premake { };
@@ -7361,8 +7323,6 @@ with pkgs;
 
   inherit (callPackages ../development/tools/parsing/ragel { }) ragelStable ragelDev;
 
-  redis-dump = callPackage ../development/tools/redis-dump { };
-
   inherit (regclient) regbot regctl regsync;
 
   reno = with python312Packages; toPythonApplication reno;
@@ -7562,8 +7522,6 @@ with pkgs;
 
   appstream = callPackage ../development/libraries/appstream { };
 
-  apr = callPackage ../development/libraries/apr { };
-
   argparse-manpage = with python3Packages; toPythonApplication argparse-manpage;
 
   asio_1_10 = callPackage ../development/libraries/asio/1.10.nix { };
@@ -7640,10 +7598,6 @@ with pkgs;
     };
   });
 
-  hercules-ci-agent = callPackage ../development/tools/continuous-integration/hercules-ci-agent { };
-
-  hci = callPackage ../development/tools/continuous-integration/hci { };
-
   niv = lib.getBin (haskell.lib.compose.justStaticExecutables haskellPackages.niv);
 
   ormolu = lib.getBin (haskell.lib.compose.justStaticExecutables haskellPackages.ormolu);
@@ -8201,8 +8155,6 @@ with pkgs;
 
   highfive-mpi = highfive.override { hdf5 = hdf5-mpi; };
 
-  hivex = callPackage ../development/libraries/hivex { };
-
   hspell = callPackage ../development/libraries/hspell { };
 
   hspellDicts = callPackage ../development/libraries/hspell/dicts.nix { };
@@ -8334,8 +8286,6 @@ with pkgs;
     }
   );
 
-  laurel = callPackage ../servers/monitoring/laurel/default.nix { };
-
   lcms = lcms2;
 
   libagar = callPackage ../development/libraries/libagar { };
@@ -8468,8 +8418,6 @@ with pkgs;
     inherit (lomiri) cmake-extras;
   };
 
-  librepo = callPackage ../tools/package-management/librepo { };
-
   libretranslate = with python3.pkgs; toPythonApplication libretranslate;
 
   librsb = callPackage ../development/libraries/librsb {
@@ -9867,10 +9815,6 @@ with pkgs;
 
   ### SERVERS
 
-  alerta = callPackage ../servers/monitoring/alerta/client.nix { };
-
-  alerta-server = callPackage ../servers/monitoring/alerta { };
-
   apacheHttpd_2_4 = callPackage ../servers/http/apache-httpd/2.4.nix { };
   apacheHttpd = apacheHttpd_2_4;
 
@@ -9951,8 +9895,6 @@ with pkgs;
   dnsutils = bind.dnsutils;
   dig = lib.addMetaAttrs { mainProgram = "dig"; } bind.dnsutils;
 
-  charybdis = callPackage ../servers/irc/charybdis { };
-
   clickhouse-cli = with python3Packages; toPythonApplication clickhouse-cli;
 
   couchdb3 = callPackage ../servers/http/couchdb/3.nix {
@@ -9998,8 +9940,6 @@ with pkgs;
     jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
   };
 
-  eventstore = callPackage ../servers/nosql/eventstore { };
-
   felix = callPackage ../servers/felix { };
 
   felix_remoteshell = callPackage ../servers/felix/remoteshell.nix { };
@@ -10016,8 +9956,6 @@ with pkgs;
   grafana = callPackage ../servers/monitoring/grafana { };
   grafanaPlugins = recurseIntoAttrs (callPackages ../servers/monitoring/grafana/plugins { });
 
-  hasura-cli = callPackage ../servers/hasura/cli.nix { };
-
   inherit (callPackage ../servers/hbase { })
     hbase_2_4
     hbase_2_5
@@ -10320,8 +10258,6 @@ with pkgs;
 
   nagiosPlugins = recurseIntoAttrs (callPackages ../servers/monitoring/nagios-plugins { });
 
-  riemann-dash = callPackage ../servers/monitoring/riemann-dash { };
-
   qboot = pkgsi686Linux.callPackage ../applications/virtualization/qboot { };
 
   rust-hypervisor-firmware = callPackage ../applications/virtualization/rust-hypervisor-firmware { };
@@ -13322,8 +13258,6 @@ with pkgs;
 
   sfxr-qt = libsForQt5.callPackage ../applications/audio/sfxr-qt { };
 
-  sommelier = callPackage ../applications/window-managers/sommelier { };
-
   spotify-qt = qt6Packages.callPackage ../applications/audio/spotify-qt { };
 
   sonic-pi = libsForQt5.callPackage ../applications/audio/sonic-pi { };
@@ -13655,8 +13589,6 @@ with pkgs;
 
   vdirsyncer = with python3Packages; toPythonApplication vdirsyncer;
 
-  veusz = callPackage ../applications/graphics/veusz { };
-
   vim = vimUtils.makeCustomizable (
     callPackage ../applications/editors/vim {
     }
@@ -13777,8 +13709,6 @@ with pkgs;
     onlyLibVLC = true;
   };
 
-  vorbis-tools = callPackage ../applications/audio/vorbis-tools { };
-
   vscode = callPackage ../applications/editors/vscode/vscode.nix { };
   vscode-fhs = vscode.fhs;
   vscode-fhsWithPackages = vscode.fhsWithPackages;
@@ -14465,8 +14395,6 @@ with pkgs;
   npush = callPackage ../games/npush { };
   run-npush = callPackage ../games/npush/run.nix { };
 
-  oilrush = callPackage ../games/oilrush { };
-
   openloco = pkgsi686Linux.callPackage ../games/openloco { };
 
   openmw = libsForQt5.callPackage ../games/openmw { };
@@ -14825,12 +14753,6 @@ with pkgs;
 
   avogadro2 = libsForQt5.callPackage ../applications/science/chemistry/avogadro2 { };
 
-  jmol = callPackage ../applications/science/chemistry/jmol {
-    jre = jre8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
-  };
-
-  marvin = callPackage ../applications/science/chemistry/marvin { };
-
   molbar = with python3Packages; toPythonApplication molbar;
 
   nwchem = callPackage ../applications/science/chemistry/nwchem {
@@ -14906,8 +14828,6 @@ with pkgs;
     };
   };
 
-  truvari = callPackage ../applications/science/biology/truvari { };
-
   ### SCIENCE/MACHINE LEARNING
 
   sc2-headless = callPackage ../applications/science/machine-learning/sc2-headless { };
@@ -16019,8 +15939,6 @@ with pkgs;
     pinentry = pinentry-curses;
   };
 
-  maphosts = callPackage ../tools/networking/maphosts { };
-
   tora = libsForQt5.callPackage ../development/tools/tora { };
 
   nitrokey-app = libsForQt5.callPackage ../tools/security/nitrokey-app { };