diff --git a/doc/doc-support/include-to-nav.py b/doc/doc-support/include-to-nav.py
index d78f61e2674e..1878c6663e3d 100755
--- a/doc/doc-support/include-to-nav.py
+++ b/doc/doc-support/include-to-nav.py
@@ -6,9 +6,10 @@ from typing import TypedDict
 
 # Coupled to where this file lives!
 # Needed to resolve the relative includes file paths
-DOC_ROOT = Path(__file__).resolve().parent.parent
+REPO_ROOT = Path(__file__).resolve().parent.parent.parent
 
-ROOT_FILE = DOC_ROOT / "manual.md.in"
+ROOT_FILE = REPO_ROOT / "nixos/doc/manual/manual.md"
+DOC_ROOT = ROOT_FILE.parent
 
 INCLUDE_RE = re.compile(r"^```\{=include=\}(?P<rest>.*)$")
 FENCE_RE = re.compile(r"^(```|~~~)")
diff --git a/nixos/doc/manual/administration/containers.chapter.md b/nixos/doc/manual/administration/containers.chapter.md
index 50493b562b54..85acccbdeb65 100644
--- a/nixos/doc/manual/administration/containers.chapter.md
+++ b/nixos/doc/manual/administration/containers.chapter.md
@@ -20,9 +20,3 @@ get upgraded along with your host system when you run `nixos-rebuild`,
 which is often not what you want. By contrast, in the imperative
 approach, containers are configured and updated independently from the
 host system.
-
-```{=include=} sections
-imperative-containers.section.md
-declarative-containers.section.md
-container-networking.section.md
-```
diff --git a/nixos/doc/manual/administration/running.md b/nixos/doc/manual/administration/running.md
index 83412d9b7af5..ec5181c7997c 100644
--- a/nixos/doc/manual/administration/running.md
+++ b/nixos/doc/manual/administration/running.md
@@ -1,15 +1,3 @@
 # Administration {#ch-running}
 
 This chapter describes various aspects of managing a running NixOS system, such as how to use the {command}`systemd` service manager.
-
-```{=include=} chapters
-service-mgmt.chapter.md
-rebooting.chapter.md
-user-sessions.chapter.md
-control-groups.chapter.md
-logging.chapter.md
-system-state.chapter.md
-cleaning-store.chapter.md
-containers.chapter.md
-troubleshooting.chapter.md
-```
diff --git a/nixos/doc/manual/administration/system-state.chapter.md b/nixos/doc/manual/administration/system-state.chapter.md
index 89013933cda5..8a814308b4d4 100644
--- a/nixos/doc/manual/administration/system-state.chapter.md
+++ b/nixos/doc/manual/administration/system-state.chapter.md
@@ -8,10 +8,3 @@ However, it is possible and not-uncommon to create [impermanent systems], whose
 this kind of configuration, special care needs to be taken.
 
 [impermanent systems]: https://wiki.nixos.org/wiki/Impermanence
-
-
-```{=include=} sections
-nixos-state.section.md
-systemd-state.section.md
-zfs-state.section.md
-```
diff --git a/nixos/doc/manual/administration/troubleshooting.chapter.md b/nixos/doc/manual/administration/troubleshooting.chapter.md
index 1253607f8efc..4fabbc960f2d 100644
--- a/nixos/doc/manual/administration/troubleshooting.chapter.md
+++ b/nixos/doc/manual/administration/troubleshooting.chapter.md
@@ -2,11 +2,3 @@
 
 This chapter describes solutions to common problems you might encounter
 when you manage your NixOS system.
-
-```{=include=} sections
-boot-problems.section.md
-maintenance-mode.section.md
-rollback.section.md
-store-corruption.section.md
-network-problems.section.md
-```
diff --git a/nixos/doc/manual/configuration/config-syntax.chapter.md b/nixos/doc/manual/configuration/config-syntax.chapter.md
index 9e606b2b82af..de5e2a5d0948 100644
--- a/nixos/doc/manual/configuration/config-syntax.chapter.md
+++ b/nixos/doc/manual/configuration/config-syntax.chapter.md
@@ -10,9 +10,3 @@ of the Nix language are fully described in the [Nix
 manual](https://nixos.org/nix/manual/#chap-writing-nix-expressions), but
 here we give a short overview of the most important constructs useful in
 NixOS configuration files.
-
-```{=include=} sections
-config-file.section.md
-abstractions.section.md
-modularity.section.md
-```
diff --git a/nixos/doc/manual/configuration/configuration.md b/nixos/doc/manual/configuration/configuration.md
index fae8874b8323..12d0109bbf38 100644
--- a/nixos/doc/manual/configuration/configuration.md
+++ b/nixos/doc/manual/configuration/configuration.md
@@ -2,27 +2,4 @@
 
 This chapter describes how to configure various aspects of a NixOS machine through the configuration file {file}`/etc/nixos/configuration.nix`. As described in [](#sec-changing-config), changes to this file only take effect after you run {command}`nixos-rebuild`.
 
-```{=include=} chapters
-config-syntax.chapter.md
-package-mgmt.chapter.md
-user-mgmt.chapter.md
-file-systems.chapter.md
-x-windows.chapter.md
-wayland.chapter.md
-gpu-accel.chapter.md
-xfce.chapter.md
-networking.chapter.md
-linux-kernel.chapter.md
-subversion.chapter.md
-```
-
-```{=include=} chapters
-@MODULE_CHAPTERS@
-```
-
-```{=include=} chapters
-profiles.chapter.md
-mattermost.chapter.md
-kubernetes.chapter.md
-```
 <!-- Apache; libvirtd virtualisation -->
diff --git a/nixos/doc/manual/configuration/declarative-packages.section.md b/nixos/doc/manual/configuration/declarative-packages.section.md
index 23d03010da03..9dd9c2963f6f 100644
--- a/nixos/doc/manual/configuration/declarative-packages.section.md
+++ b/nixos/doc/manual/configuration/declarative-packages.section.md
@@ -39,8 +39,3 @@ configuration, use `pkgs` prefix (variable).
 
 To "uninstall" a package, remove it from
 [](#opt-environment.systemPackages) and run `nixos-rebuild switch`.
-
-```{=include=} sections
-customizing-packages.section.md
-adding-custom-packages.section.md
-```
diff --git a/nixos/doc/manual/configuration/file-systems.chapter.md b/nixos/doc/manual/configuration/file-systems.chapter.md
index 8b6a06c5720a..4c63bde731f9 100644
--- a/nixos/doc/manual/configuration/file-systems.chapter.md
+++ b/nixos/doc/manual/configuration/file-systems.chapter.md
@@ -37,10 +37,3 @@ System startup will fail if any of the filesystems fails to mount,
 dropping you to the emergency shell. You can make a mount asynchronous
 and non-critical by adding `options = [ "nofail" ];`.
 :::
-
-```{=include=} sections
-luks-file-systems.section.md
-sshfs-file-systems.section.md
-nfs-file-systems.section.md
-overlayfs.section.md
-```
diff --git a/nixos/doc/manual/configuration/networking.chapter.md b/nixos/doc/manual/configuration/networking.chapter.md
index abbd9766f173..b2474d029363 100644
--- a/nixos/doc/manual/configuration/networking.chapter.md
+++ b/nixos/doc/manual/configuration/networking.chapter.md
@@ -3,14 +3,4 @@
 This section describes how to configure networking components
 on your NixOS machine.
 
-```{=include=} sections
-network-manager.section.md
-ssh.section.md
-ipv4-config.section.md
-ipv6-config.section.md
-firewall.section.md
-wireless.section.md
-ad-hoc-network-config.section.md
-renaming-interfaces.section.md
-```
 <!-- TODO: OpenVPN, NAT -->
diff --git a/nixos/doc/manual/configuration/package-mgmt.chapter.md b/nixos/doc/manual/configuration/package-mgmt.chapter.md
index 1148bbe84740..d59a491d61b7 100644
--- a/nixos/doc/manual/configuration/package-mgmt.chapter.md
+++ b/nixos/doc/manual/configuration/package-mgmt.chapter.md
@@ -11,8 +11,3 @@ NixOS has two distinct styles of package management:
 -   *Ad hoc*, where you install, upgrade and uninstall packages via the
     `nix-env` command. This style allows mixing packages from different
     Nixpkgs versions. It's the only choice for non-root users.
-
-```{=include=} sections
-declarative-packages.section.md
-ad-hoc-packages.section.md
-```
diff --git a/nixos/doc/manual/configuration/profiles.chapter.md b/nixos/doc/manual/configuration/profiles.chapter.md
index dda65add46d9..b173a01e6b39 100644
--- a/nixos/doc/manual/configuration/profiles.chapter.md
+++ b/nixos/doc/manual/configuration/profiles.chapter.md
@@ -16,17 +16,3 @@ install media, many are actually intended to be used in real installs.
 
 What follows is a brief explanation of the purpose and use-case for each
 profile. Detailing each option configured by each one is out of scope.
-
-```{=include=} sections
-profiles/all-hardware.section.md
-profiles/base.section.md
-profiles/clone-config.section.md
-profiles/demo.section.md
-profiles/docker-container.section.md
-profiles/graphical.section.md
-profiles/headless.section.md
-profiles/installation-device.section.md
-profiles/perlless.section.md
-profiles/minimal.section.md
-profiles/qemu-guest.section.md
-```
diff --git a/nixos/doc/manual/default.nix b/nixos/doc/manual/default.nix
index e9ecc6c02bff..18ff9b56abbd 100644
--- a/nixos/doc/manual/default.nix
+++ b/nixos/doc/manual/default.nix
@@ -103,12 +103,16 @@ let
 
     cp -r ${../../../doc/release-notes} ./release-notes-nixpkgs
 
+    cp ${./nav.json} nav.json
+
     substituteInPlace ./manual.md \
       --replace-fail '@NIXOS_VERSION@' "${version}"
-    substituteInPlace ./configuration/configuration.md \
+    substituteInPlace ./nav.json \
       --replace-fail \
-          '@MODULE_CHAPTERS@' \
-          ${escapeShellArg (concatMapStringsSep "\n" (p: "${p.value}") config.meta.doc)}
+          '"@MODULE_CHAPTERS@"' \
+          ${escapeShellArg (
+            concatMapStringsSep ",\n" (p: ''{ "file": "${p.value}" }'') config.meta.doc
+          )}
     substituteInPlace ./nixos-options.md \
       --replace-fail \
         '@NIXOS_OPTIONS_JSON@' \
@@ -200,9 +204,10 @@ rec {
           --script ./highlightjs/loader.js \
           --script ./anchor.min.js \
           --script ./anchor-use.js \
-          --sidebar-depth 2 \
+          --sidebar-depth 3 \
           --header ${./header.html}\
           --no-navheader \
+          --experimental-config nav.json \
           ./manual.md \
           $dst/${common.indexPath}
 
diff --git a/nixos/doc/manual/development/development.md b/nixos/doc/manual/development/development.md
index 37762afb41da..198773ef768c 100644
--- a/nixos/doc/manual/development/development.md
+++ b/nixos/doc/manual/development/development.md
@@ -1,16 +1,3 @@
 # Development {#ch-development}
 
 This chapter describes how you can modify and extend NixOS.
-
-```{=include=} chapters
-sources.chapter.md
-writing-modules.chapter.md
-building-parts.chapter.md
-bootspec.chapter.md
-what-happens-during-a-system-switch.chapter.md
-writing-documentation.chapter.md
-nixos-tests.chapter.md
-developing-the-test-driver.chapter.md
-testing-installer.chapter.md
-modular-services.md
-```
diff --git a/nixos/doc/manual/development/nixos-tests.chapter.md b/nixos/doc/manual/development/nixos-tests.chapter.md
index 889a90bae68b..4f4cfd481c8e 100644
--- a/nixos/doc/manual/development/nixos-tests.chapter.md
+++ b/nixos/doc/manual/development/nixos-tests.chapter.md
@@ -4,11 +4,3 @@ When you add some feature to NixOS, you should write a test for it.
 NixOS tests are kept in the directory `nixos/tests`, and are executed
 (using Nix) by a testing framework that automatically starts one or more
 virtual machines containing the NixOS system(s) required for the test.
-
-```{=include=} sections
-writing-nixos-tests.section.md
-running-nixos-tests.section.md
-running-nixos-tests-interactively.section.md
-linking-nixos-tests-to-packages.section.md
-testing-hardware-features.section.md
-```
diff --git a/nixos/doc/manual/development/what-happens-during-a-system-switch.chapter.md b/nixos/doc/manual/development/what-happens-during-a-system-switch.chapter.md
index 973f7c47899a..2aedb08e2a97 100644
--- a/nixos/doc/manual/development/what-happens-during-a-system-switch.chapter.md
+++ b/nixos/doc/manual/development/what-happens-during-a-system-switch.chapter.md
@@ -53,10 +53,3 @@ More detailed output can be displayed by setting `STC_DEBUG=1`.
 Most of these actions are either self-explaining but some of them have to do
 with our units or the activation script. For this reason, these topics are
 explained in the next sections.
-
-```{=include=} sections
-unit-handling.section.md
-activation-script.section.md
-non-switchable-systems.section.md
-etc-overlay.section.md
-```
diff --git a/nixos/doc/manual/development/writing-modules.chapter.md b/nixos/doc/manual/development/writing-modules.chapter.md
index 626834fc3e66..fe06af5c9893 100644
--- a/nixos/doc/manual/development/writing-modules.chapter.md
+++ b/nixos/doc/manual/development/writing-modules.chapter.md
@@ -209,16 +209,3 @@ in
 }
 ```
 :::
-
-```{=include=} sections
-option-declarations.section.md
-option-types.section.md
-option-def.section.md
-assertions.section.md
-meta-attributes.section.md
-importing-modules.section.md
-replace-modules.section.md
-freeform-modules.section.md
-settings-options.section.md
-state-revision.section.md
-```
diff --git a/nixos/doc/manual/installation/installation.md b/nixos/doc/manual/installation/installation.md
index 04bad5be1d46..7310e8bda5ee 100644
--- a/nixos/doc/manual/installation/installation.md
+++ b/nixos/doc/manual/installation/installation.md
@@ -1,13 +1,3 @@
 # Installation {#ch-installation}
 
 This section describes how to obtain, install, and configure NixOS for first-time use.
-
-```{=include=} chapters
-obtaining.chapter.md
-installing.chapter.md
-changing-config.chapter.md
-upgrading.chapter.md
-building-nixos.chapter.md
-building-images-via-nixos-rebuild-build-image.chapter.md
-building-images-via-systemd-repart.chapter.md
-```
diff --git a/nixos/doc/manual/installation/installing.chapter.md b/nixos/doc/manual/installation/installing.chapter.md
index 402c285d4456..efaf887997f0 100644
--- a/nixos/doc/manual/installation/installing.chapter.md
+++ b/nixos/doc/manual/installation/installing.chapter.md
@@ -577,12 +577,3 @@ With a partitioned disk.
 :::
 
 ## Additional installation notes {#sec-installation-additional-notes}
-
-```{=include=} sections
-installing-usb.section.md
-installing-pxe.section.md
-installing-kexec.section.md
-installing-virtualbox-guest.section.md
-installing-from-other-distro.section.md
-installing-behind-a-proxy.section.md
-```
diff --git a/nixos/doc/manual/manual.md b/nixos/doc/manual/manual.md
index 4fc39ffc785b..604b61c34502 100644
--- a/nixos/doc/manual/manual.md
+++ b/nixos/doc/manual/manual.md
@@ -32,21 +32,6 @@
 
 -->
 
-```{=include=} preface
-preface.md
-```
-
-```{=include=} parts
-installation/installation.md
-configuration/configuration.md
-administration/running.md
-development/development.md
-```
-
-```{=include=} chapters
-contributing-to-this-manual.chapter.md
-```
-
 ```{=include=} appendix html:into-file=//options.html
 nixos-options.md
 ```
diff --git a/nixos/doc/manual/nav.json b/nixos/doc/manual/nav.json
new file mode 100644
index 000000000000..91bd93a503d0
--- /dev/null
+++ b/nixos/doc/manual/nav.json
@@ -0,0 +1,444 @@
+{
+  "open": [],
+  "items": [
+    {
+      "file": "preface.md"
+    },
+    {
+      "label": "Installation",
+      "id": "ch-installation",
+      "children": [
+        {
+          "file": "installation/installation.md"
+        },
+        {
+          "file": "installation/obtaining.chapter.md"
+        },
+        {
+          "label": "Installing NixOS",
+          "id": "sec-installation",
+          "children": [
+            {
+              "file": "installation/installing.chapter.md"
+            },
+            {
+              "file": "installation/installing-usb.section.md"
+            },
+            {
+              "file": "installation/installing-pxe.section.md"
+            },
+            {
+              "file": "installation/installing-kexec.section.md"
+            },
+            {
+              "file": "installation/installing-virtualbox-guest.section.md"
+            },
+            {
+              "file": "installation/installing-from-other-distro.section.md"
+            },
+            {
+              "file": "installation/installing-behind-a-proxy.section.md"
+            }
+          ]
+        },
+        {
+          "file": "installation/changing-config.chapter.md"
+        },
+        {
+          "file": "installation/upgrading.chapter.md"
+        },
+        {
+          "file": "installation/building-nixos.chapter.md"
+        },
+        {
+          "file": "installation/building-images-via-nixos-rebuild-build-image.chapter.md"
+        },
+        {
+          "file": "installation/building-images-via-systemd-repart.chapter.md"
+        }
+      ]
+    },
+    {
+      "label": "Configuration",
+      "id": "ch-configuration",
+      "children": [
+        {
+          "file": "configuration/configuration.md"
+        },
+        {
+          "label": "Configuration Syntax",
+          "id": "sec-configuration-syntax",
+          "children": [
+            {
+              "file": "configuration/config-syntax.chapter.md"
+            },
+            {
+              "file": "configuration/config-file.section.md"
+            },
+            {
+              "file": "configuration/abstractions.section.md"
+            },
+            {
+              "file": "configuration/modularity.section.md"
+            }
+          ]
+        },
+        {
+          "label": "Package Management",
+          "id": "sec-package-management",
+          "children": [
+            {
+              "file": "configuration/package-mgmt.chapter.md"
+            },
+            {
+              "label": "Declarative Package Management",
+              "id": "sec-declarative-package-mgmt",
+              "children": [
+                {
+                  "file": "configuration/declarative-packages.section.md"
+                },
+                {
+                  "file": "configuration/customizing-packages.section.md"
+                },
+                {
+                  "file": "configuration/adding-custom-packages.section.md"
+                }
+              ]
+            },
+            {
+              "file": "configuration/ad-hoc-packages.section.md"
+            }
+          ]
+        },
+        {
+          "file": "configuration/user-mgmt.chapter.md"
+        },
+        {
+          "label": "File Systems",
+          "id": "ch-file-systems",
+          "children": [
+            {
+              "file": "configuration/file-systems.chapter.md"
+            },
+            {
+              "file": "configuration/luks-file-systems.section.md"
+            },
+            {
+              "file": "configuration/sshfs-file-systems.section.md"
+            },
+            {
+              "file": "configuration/nfs-file-systems.section.md"
+            },
+            {
+              "file": "configuration/overlayfs.section.md"
+            }
+          ]
+        },
+        {
+          "file": "configuration/x-windows.chapter.md"
+        },
+        {
+          "file": "configuration/wayland.chapter.md"
+        },
+        {
+          "file": "configuration/gpu-accel.chapter.md"
+        },
+        {
+          "file": "configuration/xfce.chapter.md"
+        },
+        {
+          "label": "Networking",
+          "id": "sec-networking",
+          "children": [
+            {
+              "file": "configuration/networking.chapter.md"
+            },
+            {
+              "file": "configuration/network-manager.section.md"
+            },
+            {
+              "file": "configuration/ssh.section.md"
+            },
+            {
+              "file": "configuration/ipv4-config.section.md"
+            },
+            {
+              "file": "configuration/ipv6-config.section.md"
+            },
+            {
+              "file": "configuration/firewall.section.md"
+            },
+            {
+              "file": "configuration/wireless.section.md"
+            },
+            {
+              "file": "configuration/ad-hoc-network-config.section.md"
+            },
+            {
+              "file": "configuration/renaming-interfaces.section.md"
+            }
+          ]
+        },
+        {
+          "file": "configuration/linux-kernel.chapter.md"
+        },
+        {
+          "file": "configuration/subversion.chapter.md"
+        },
+        "@MODULE_CHAPTERS@",
+        {
+          "label": "Profiles",
+          "id": "ch-profiles",
+          "children": [
+            {
+              "file": "configuration/profiles.chapter.md"
+            },
+            {
+              "file": "configuration/profiles/all-hardware.section.md"
+            },
+            {
+              "file": "configuration/profiles/base.section.md"
+            },
+            {
+              "file": "configuration/profiles/clone-config.section.md"
+            },
+            {
+              "file": "configuration/profiles/demo.section.md"
+            },
+            {
+              "file": "configuration/profiles/docker-container.section.md"
+            },
+            {
+              "file": "configuration/profiles/graphical.section.md"
+            },
+            {
+              "file": "configuration/profiles/headless.section.md"
+            },
+            {
+              "file": "configuration/profiles/installation-device.section.md"
+            },
+            {
+              "file": "configuration/profiles/perlless.section.md"
+            },
+            {
+              "file": "configuration/profiles/minimal.section.md"
+            },
+            {
+              "file": "configuration/profiles/qemu-guest.section.md"
+            }
+          ]
+        },
+        {
+          "file": "configuration/mattermost.chapter.md"
+        },
+        {
+          "file": "configuration/kubernetes.chapter.md"
+        }
+      ]
+    },
+    {
+      "label": "Administration",
+      "id": "ch-running",
+      "children": [
+        {
+          "file": "administration/running.md"
+        },
+        {
+          "file": "administration/service-mgmt.chapter.md"
+        },
+        {
+          "file": "administration/rebooting.chapter.md"
+        },
+        {
+          "file": "administration/user-sessions.chapter.md"
+        },
+        {
+          "file": "administration/control-groups.chapter.md"
+        },
+        {
+          "file": "administration/logging.chapter.md"
+        },
+        {
+          "label": "Necessary system state",
+          "id": "ch-system-state",
+          "children": [
+            {
+              "file": "administration/system-state.chapter.md"
+            },
+            {
+              "file": "administration/nixos-state.section.md"
+            },
+            {
+              "file": "administration/systemd-state.section.md"
+            },
+            {
+              "file": "administration/zfs-state.section.md"
+            }
+          ]
+        },
+        {
+          "file": "administration/cleaning-store.chapter.md"
+        },
+        {
+          "label": "Container Management",
+          "id": "ch-containers",
+          "children": [
+            {
+              "file": "administration/containers.chapter.md"
+            },
+            {
+              "file": "administration/imperative-containers.section.md"
+            },
+            {
+              "file": "administration/declarative-containers.section.md"
+            },
+            {
+              "file": "administration/container-networking.section.md"
+            }
+          ]
+        },
+        {
+          "label": "Troubleshooting",
+          "id": "ch-troubleshooting",
+          "children": [
+            {
+              "file": "administration/troubleshooting.chapter.md"
+            },
+            {
+              "file": "administration/boot-problems.section.md"
+            },
+            {
+              "file": "administration/maintenance-mode.section.md"
+            },
+            {
+              "file": "administration/rollback.section.md"
+            },
+            {
+              "file": "administration/store-corruption.section.md"
+            },
+            {
+              "file": "administration/network-problems.section.md"
+            }
+          ]
+        }
+      ]
+    },
+    {
+      "label": "Development",
+      "id": "ch-development",
+      "children": [
+        {
+          "file": "development/development.md"
+        },
+        {
+          "file": "development/sources.chapter.md"
+        },
+        {
+          "label": "Writing NixOS Modules",
+          "id": "sec-writing-modules",
+          "children": [
+            {
+              "file": "development/writing-modules.chapter.md"
+            },
+            {
+              "file": "development/option-declarations.section.md"
+            },
+            {
+              "file": "development/option-types.section.md"
+            },
+            {
+              "file": "development/option-def.section.md"
+            },
+            {
+              "file": "development/assertions.section.md"
+            },
+            {
+              "file": "development/meta-attributes.section.md"
+            },
+            {
+              "file": "development/importing-modules.section.md"
+            },
+            {
+              "file": "development/replace-modules.section.md"
+            },
+            {
+              "file": "development/freeform-modules.section.md"
+            },
+            {
+              "file": "development/settings-options.section.md"
+            },
+            {
+              "file": "development/state-revision.section.md"
+            }
+          ]
+        },
+        {
+          "file": "development/building-parts.chapter.md"
+        },
+        {
+          "file": "development/bootspec.chapter.md"
+        },
+        {
+          "label": "What happens during a system switch?",
+          "id": "sec-switching-systems",
+          "children": [
+            {
+              "file": "development/what-happens-during-a-system-switch.chapter.md"
+            },
+            {
+              "file": "development/unit-handling.section.md"
+            },
+            {
+              "file": "development/activation-script.section.md"
+            },
+            {
+              "file": "development/non-switchable-systems.section.md"
+            },
+            {
+              "file": "development/etc-overlay.section.md"
+            }
+          ]
+        },
+        {
+          "file": "development/writing-documentation.chapter.md"
+        },
+        {
+          "label": "NixOS Tests",
+          "id": "sec-nixos-tests",
+          "children": [
+            {
+              "file": "development/nixos-tests.chapter.md"
+            },
+            {
+              "file": "development/writing-nixos-tests.section.md"
+            },
+            {
+              "file": "development/running-nixos-tests.section.md"
+            },
+            {
+              "file": "development/running-nixos-tests-interactively.section.md"
+            },
+            {
+              "file": "development/linking-nixos-tests-to-packages.section.md"
+            },
+            {
+              "file": "development/testing-hardware-features.section.md"
+            }
+          ]
+        },
+        {
+          "file": "development/developing-the-test-driver.chapter.md"
+        },
+        {
+          "file": "development/testing-installer.chapter.md"
+        },
+        {
+          "file": "development/modular-services.md"
+        }
+      ]
+    },
+    {
+      "file": "contributing-to-this-manual.chapter.md"
+    }
+  ]
+}
diff --git a/pkgs/applications/editors/vim/plugins/generated.nix b/pkgs/applications/editors/vim/plugins/generated.nix
index 14a78fd0e267..a3cb7438564c 100644
--- a/pkgs/applications/editors/vim/plugins/generated.nix
+++ b/pkgs/applications/editors/vim/plugins/generated.nix
@@ -461,12 +461,12 @@ final: prev: {
 
   SchemaStore-nvim = buildVimPlugin {
     pname = "SchemaStore.nvim";
-    version = "0-unstable-2026-09-12";
+    version = "0-unstable-2026-09-16";
     src = fetchFromGitHub {
       owner = "b0o";
       repo = "SchemaStore.nvim";
-      rev = "05e938c0aa5dfbdbb11972fa4c8a85f27f402ba0";
-      hash = "sha256-p+h2y42PRUM1ZPIlBe31/n7IPmh3oEiWgL3HuoUI8Yg=";
+      rev = "ab094b7f788231fe9b68deac78c3d512302c58a6";
+      hash = "sha256-AKGx8ubYHhDireMwOcimvr7zpM1sjytkaRHtguAfVLo=";
     };
     meta.homepage = "https://github.com/b0o/SchemaStore.nvim/";
     meta.license = getLicenseFromSpdxId "Apache-2.0";
@@ -1135,12 +1135,12 @@ final: prev: {
 
   async-nvim = buildVimPlugin {
     pname = "async.nvim";
-    version = "0-unstable-2026-09-03";
+    version = "0-unstable-2026-09-16";
     src = fetchFromGitHub {
       owner = "lewis6991";
       repo = "async.nvim";
-      rev = "ca8f5696c45bd4786b8840923d86b6932ce92ded";
-      hash = "sha256-dUP9knuzL4qiXdbcjil3Yu5Ve3sVL1DSKJbEY5FwDpA=";
+      rev = "15f28ec323a75f34f317336831c00c2d1b0a7192";
+      hash = "sha256-8S2HNBBwB3c58NudCGrTyBKoQkGDIG0Syravh+sl/Dw=";
     };
     meta.homepage = "https://github.com/lewis6991/async.nvim/";
     meta.license = getLicenseFromSpdxId "MIT";
@@ -3513,12 +3513,12 @@ final: prev: {
 
   coc-nvim = buildVimPlugin {
     pname = "coc.nvim";
-    version = "0.0.82-unstable-2026-09-11";
+    version = "0.0.82-unstable-2026-09-16";
     src = fetchFromGitHub {
       owner = "neoclide";
       repo = "coc.nvim";
-      rev = "90b55f067595e7f9dd920c957d6345f434f32dd2";
-      hash = "sha256-6gX6voB7AZhBmG/NYUCEwEm6V5gunT+WHVSvOsZ0Kj4=";
+      rev = "c39eba4cf90254dd9e3ce54f617f07d1853d5da5";
+      hash = "sha256-FMP/UaBSAj29Cei7CDLamtjOAOAqcZLGBYjt/6uQHlI=";
     };
     meta.homepage = "https://github.com/neoclide/coc.nvim/";
     meta.license = getLicenseFromSpdxId "MIT";
@@ -3611,12 +3611,12 @@ final: prev: {
 
   codecompanion-nvim = buildVimPlugin {
     pname = "codecompanion.nvim";
-    version = "19.24.1";
+    version = "19.25.0";
     src = fetchFromGitHub {
       owner = "olimorris";
       repo = "codecompanion.nvim";
-      tag = "v19.24.1";
-      hash = "sha256-oihHiKhU093AT5aqvTxJ4wXmH+pMKFJ5zgzUo5SJ/Yw=";
+      tag = "v19.25.0";
+      hash = "sha256-PTvllgZji45JdW1NW9YmRDJqiEvdmbpeB2QGvu10jbM=";
     };
     meta.homepage = "https://github.com/olimorris/codecompanion.nvim/";
     meta.license = getLicenseFromSpdxId "Apache-2.0";
@@ -4228,12 +4228,12 @@ final: prev: {
 
   coq_nvim = buildVimPlugin {
     pname = "coq_nvim";
-    version = "0-unstable-2026-09-04";
+    version = "0-unstable-2026-09-14";
     src = fetchFromGitHub {
       owner = "ms-jpq";
       repo = "coq_nvim";
-      rev = "a0689fdab9ad5a46bc8730c96a43f215d605f23c";
-      hash = "sha256-ZKju7Pb5GdhWVwF1oXgGt6DXZvyaaQKQHSuKce6P+DI=";
+      rev = "735596a7ec4f4984c90827f8e1100e320eb14cba";
+      hash = "sha256-igRYHOoBBz7R5aUuxPkaAfmTH6TYSXMNV2pBTcT5Pe0=";
     };
     meta.homepage = "https://github.com/ms-jpq/coq_nvim/";
     meta.license = getLicenseFromSpdxId "GPL-3.0-only";
@@ -4816,12 +4816,12 @@ final: prev: {
 
   demicolon-nvim = buildVimPlugin {
     pname = "demicolon.nvim";
-    version = "2.0-unstable-2026-06-20";
+    version = "2.0-unstable-2026-09-16";
     src = fetchFromGitHub {
       owner = "mawkler";
       repo = "demicolon.nvim";
-      rev = "153444f17494e2ff6ab7d226e6173c1841b1130a";
-      hash = "sha256-gBGJphvT1AXN/UImrSWiWhhzcQt4i68Vbwtr9jXipwo=";
+      rev = "d4bc516cc346202eb7f933b38e47534d41769f46";
+      hash = "sha256-N60NIspY5QspqvqfndU74jJDClm7uBL5VpKwnamuodM=";
     };
     meta.homepage = "https://github.com/mawkler/demicolon.nvim/";
     meta.license = getLicenseFromSpdxId "MIT";
@@ -5490,12 +5490,12 @@ final: prev: {
 
   easy-dotnet-nvim = buildVimPlugin {
     pname = "easy-dotnet.nvim";
-    version = "0-unstable-2026-09-10";
+    version = "0-unstable-2026-09-15";
     src = fetchFromGitHub {
       owner = "GustavEikaas";
       repo = "easy-dotnet.nvim";
-      rev = "bde7a1cf7c4dbad61d68b2ca41672bfe194b06f8";
-      hash = "sha256-/1FzQEXnPOl+jcj0QQ04u9lJgmDb2Ejhy3KurFpkCnU=";
+      rev = "df600029a54754d90ac35fe284b3921bb7bf1023";
+      hash = "sha256-1F1IXv3lNC7PP+fQESrQtx/7YTrMgl2SGRIAZzuxUQI=";
     };
     meta.homepage = "https://github.com/GustavEikaas/easy-dotnet.nvim/";
     meta.license = getLicenseFromSpdxId "MIT";
@@ -5799,12 +5799,12 @@ final: prev: {
 
   executor-nvim = buildVimPlugin {
     pname = "executor.nvim";
-    version = "0-unstable-2025-08-15";
+    version = "0-unstable-2026-09-15";
     src = fetchFromGitHub {
       owner = "google";
       repo = "executor.nvim";
-      rev = "56dfbe6f7fbf4a6ba7e5934df2d95810e0235f64";
-      hash = "sha256-FdcOzT3LgJBifXdEAzfMtcfrIDlYFcY1RogVxcl3Avk=";
+      rev = "f40ff80b0831c34e8feae92b996477b4bba67764";
+      hash = "sha256-UaBqJzR+s4DgtMJ2JDKhr+jJekPr8LspQvVdfgU9x/8=";
     };
     meta.homepage = "https://github.com/google/executor.nvim/";
     meta.license = getLicenseFromSpdxId "Apache-2.0";
@@ -6753,12 +6753,12 @@ final: prev: {
 
   gitignore-nvim = buildVimPlugin {
     pname = "gitignore.nvim";
-    version = "0-unstable-2025-05-30";
+    version = "0-unstable-2026-09-15";
     src = fetchFromGitHub {
       owner = "wintermute-cell";
       repo = "gitignore.nvim";
-      rev = "0344f643768c4d64af4add8c1bdddf6f7d4c9010";
-      hash = "sha256-9Qu+oVOtufvf+ekj2rY+T9c2y7BXh9d7hfl6ZiMYpPY=";
+      rev = "15ed88abbaeb5deffe6d7c6d51af9b6ff784135f";
+      hash = "sha256-45PCvabbqcgasvuFg/g8c/N6XkU43/lmqoATMnvc8NY=";
     };
     meta.homepage = "https://github.com/wintermute-cell/gitignore.nvim/";
     meta.license = getLicenseFromSpdxId "MIT";
@@ -8125,12 +8125,12 @@ final: prev: {
 
   iron-nvim = buildVimPlugin {
     pname = "iron.nvim";
-    version = "0-unstable-2026-08-30";
+    version = "0-unstable-2026-09-15";
     src = fetchFromGitHub {
       owner = "Vigemus";
       repo = "iron.nvim";
-      rev = "1ad44e4e82ad31b7df1cdb7f154c707bfd0d303c";
-      hash = "sha256-59+/yLkvBsAVmYt7HfQYn0A2oPAewAQcNx3XneyKVaQ=";
+      rev = "0168b419bc7df70cd2d97c2ec8158b6b002450b2";
+      hash = "sha256-2oQ4CGcdxVJpubxv+NQLbVk3cW38iP45xX3rAL1ZOl4=";
     };
     meta.homepage = "https://github.com/Vigemus/iron.nvim/";
     meta.license = getLicenseFromSpdxId "BSD-3-Clause";
@@ -11218,12 +11218,12 @@ final: prev: {
 
   neoconf-nvim = buildVimPlugin {
     pname = "neoconf.nvim";
-    version = "1.4.0-unstable-2026-09-03";
+    version = "1.4.0-unstable-2026-09-17";
     src = fetchFromGitHub {
       owner = "folke";
       repo = "neoconf.nvim";
-      rev = "931000cfab0120191ee914afbbc3f2b02f3533de";
-      hash = "sha256-IfL6Rbp6KIHs/QZ25kPQU2NDTkasYv4B2yiAAmbLSKg=";
+      rev = "54f249a7f1a87a51ff1f559e873daf05e20a454b";
+      hash = "sha256-tpjnVOIaULSgEzPypvKipNWlEbYvtMossbu/yhHgsWY=";
     };
     meta.homepage = "https://github.com/folke/neoconf.nvim/";
     meta.license = getLicenseFromSpdxId "Apache-2.0";
@@ -12130,12 +12130,12 @@ final: prev: {
 
   nginx-vim = buildVimPlugin {
     pname = "nginx.vim";
-    version = "1.1.0-unstable-2026-02-09";
+    version = "1.1.0-unstable-2026-09-15";
     src = fetchFromGitHub {
       owner = "chr4";
       repo = "nginx.vim";
-      rev = "a5991f38135d0c6c259d0b9f5e629ba33b891b9e";
-      hash = "sha256-rGqNjdaK5HX6Cad3x+awRLz24PfsA+APWg+vKjWn490=";
+      rev = "3f1ce6c24ba3b5bde979cfac2c017612d7bfd311";
+      hash = "sha256-7UVwoZjyfl2YiNzQnfanoqAmfmZlhRlrbtYxqrBVTGY=";
     };
     meta.homepage = "https://github.com/chr4/nginx.vim/";
     meta.license = unfree;
@@ -12409,12 +12409,12 @@ final: prev: {
 
   notmuch-nvim = buildVimPlugin {
     pname = "notmuch.nvim";
-    version = "0.4.0";
+    version = "0.5.0";
     src = fetchFromGitHub {
       owner = "yousefakbar";
       repo = "notmuch.nvim";
-      tag = "v0.4.0";
-      hash = "sha256-A+vlH8fUNd3/lTH++sp90YXRqe3/uTxOTNw43CJQQyc=";
+      tag = "v0.5.0";
+      hash = "sha256-Q2xxAC10xZFa+xKXnnyJRe5qi/aqZUwp0+l7SIIBriM=";
     };
     meta.homepage = "https://github.com/yousefakbar/notmuch.nvim/";
     meta.license = unfree;
@@ -14671,12 +14671,12 @@ final: prev: {
 
   opencode-nvim = buildVimPlugin {
     pname = "opencode.nvim";
-    version = "1.0.1";
+    version = "1.0.2";
     src = fetchFromGitHub {
       owner = "nickjvandyke";
       repo = "opencode.nvim";
-      tag = "v1.0.1";
-      hash = "sha256-rJz8AtUEgyTMvLd5cMD0wcsaNgW8FmPX1dtLymHM00o=";
+      tag = "v1.0.2";
+      hash = "sha256-AoQXcrIymg2DDHKYQFkV039bFo/AN1QJVevhsIcc/+I=";
     };
     meta.homepage = "https://github.com/nickjvandyke/opencode.nvim/";
     meta.license = getLicenseFromSpdxId "MIT";
@@ -15373,12 +15373,12 @@ final: prev: {
 
   project-nvim = buildVimPlugin {
     pname = "project.nvim";
-    version = "6.2.1-1";
+    version = "6.3.0-1";
     src = fetchFromGitHub {
       owner = "DrKJeff16";
       repo = "project.nvim";
-      tag = "v6.2.1-1";
-      hash = "sha256-jJwnMO5rYhlDp+ykL/72o4fllbtLCxdX+2ZCBJGxtwg=";
+      tag = "v6.3.0-1";
+      hash = "sha256-X8Jd6KtX/oM8Oe1KsRlixfGNAUwfkWfXQO/Xkg7EAqU=";
     };
     meta.homepage = "https://github.com/DrKJeff16/project.nvim/";
     meta.license = getLicenseFromSpdxId "Apache-2.0";
@@ -15849,12 +15849,12 @@ final: prev: {
 
   render-markdown-nvim = buildVimPlugin {
     pname = "render-markdown.nvim";
-    version = "8.13.0";
+    version = "8.14.0";
     src = fetchFromGitHub {
       owner = "MeanderingProgrammer";
       repo = "render-markdown.nvim";
-      tag = "v8.13.0";
-      hash = "sha256-ukJUaqEYI60o/lyLM5GaKsRdMW/24IZnzVzPB9/Q/zo=";
+      tag = "v8.14.0";
+      hash = "sha256-pG8lAo4qucIu+gAwrEaK79VkDFTLcuuPBYhq3sg951E=";
     };
     meta.homepage = "https://github.com/MeanderingProgrammer/render-markdown.nvim/";
     meta.license = getLicenseFromSpdxId "MIT";
@@ -18233,6 +18233,20 @@ final: prev: {
     meta.hydraPlatforms = [ ];
   };
 
+  tiny-code-action-nvim = buildVimPlugin {
+    pname = "tiny-code-action.nvim";
+    version = "0-unstable-2026-04-25";
+    src = fetchFromGitHub {
+      owner = "rachartier";
+      repo = "tiny-code-action.nvim";
+      rev = "0d040ed81f7953118b81cd12681fcdfcac069803";
+      hash = "sha256-UF9zeO5Uujdt2MEwy2d2Lhk6JRnEN4vrEvYslv0/zaA=";
+    };
+    meta.homepage = "https://github.com/rachartier/tiny-code-action.nvim/";
+    meta.license = getLicenseFromSpdxId "MIT";
+    meta.hydraPlatforms = [ ];
+  };
+
   tiny-devicons-auto-colors-nvim = buildVimPlugin {
     pname = "tiny-devicons-auto-colors.nvim";
     version = "0-unstable-2026-05-29";
@@ -26403,12 +26417,12 @@ final: prev: {
 
   zotcite = buildVimPlugin {
     pname = "zotcite";
-    version = "0.7-unstable-2026-08-24";
+    version = "0.7-unstable-2026-09-15";
     src = fetchFromGitHub {
       owner = "jalvesaq";
       repo = "zotcite";
-      rev = "282bd8963218f840d7286ce6874bafc7c6b4b535";
-      hash = "sha256-qR2/SLTUw4Mc2KpdPbkPETuvxKpOg6N3Qu3XgrNy48k=";
+      rev = "669110c668cee18565069ed8980c14af7798df0b";
+      hash = "sha256-vOO70rXJMIOH8xdP0z4E5+JU+Nx+NBYdMlYaFkU4XOs=";
     };
     meta.homepage = "https://github.com/jalvesaq/zotcite/";
     meta.license = getLicenseFromSpdxId "GPL-3.0-only";
diff --git a/pkgs/applications/editors/vim/plugins/overrides.nix b/pkgs/applications/editors/vim/plugins/overrides.nix
index c0e301bfcbe1..c0658ec8b50f 100644
--- a/pkgs/applications/editors/vim/plugins/overrides.nix
+++ b/pkgs/applications/editors/vim/plugins/overrides.nix
@@ -4655,6 +4655,13 @@ assertNoAdditions {
     };
   });
 
+  tiny-code-action-nvim = super.tiny-code-action-nvim.overrideAttrs {
+    nvimSkipModules = [
+      # test for optional previewer
+      "tiny-code-action.previewers.snacks"
+    ];
+  };
+
   tmux-complete-vim = super.tmux-complete-vim.overrideAttrs {
     # Vim plugin with optional nvim-compe lua module
     nvimSkipModules = [ "compe_tmux" ];
diff --git a/pkgs/applications/editors/vim/plugins/vim-plugin-names b/pkgs/applications/editors/vim/plugins/vim-plugin-names
index 0547218c3f45..041b12d5e4ac 100644
--- a/pkgs/applications/editors/vim/plugins/vim-plugin-names
+++ b/pkgs/applications/editors/vim/plugins/vim-plugin-names
@@ -1300,6 +1300,7 @@ https://github.com/levouh/tint.nvim/,,
 https://github.com/tinted-theming/tinted-nvim/,,
 https://github.com/tinted-theming/tinted-vim/,,
 https://github.com/rachartier/tiny-cmdline.nvim/,,
+https://github.com/rachartier/tiny-code-action.nvim/,,
 https://github.com/rachartier/tiny-devicons-auto-colors.nvim/,,
 https://github.com/rachartier/tiny-glimmer.nvim/,,
 https://github.com/rachartier/tiny-inline-diagnostic.nvim/,,
diff --git a/pkgs/applications/virtualization/virtualbox/default.nix b/pkgs/applications/virtualization/virtualbox/default.nix
index d59a17d4717f..d3044d5e5ab4 100644
--- a/pkgs/applications/virtualization/virtualbox/default.nix
+++ b/pkgs/applications/virtualization/virtualbox/default.nix
@@ -72,9 +72,9 @@ let
   buildType = "release";
   # Use maintainers/scripts/update.nix to update the version and all related hashes or
   # change the hashes in extpack.nix and guest-additions/default.nix as well manually.
-  virtualboxVersion = "7.2.16";
+  virtualboxVersion = "7.2.18";
   virtualboxSubVersion = "";
-  virtualboxSha256 = "50356ccdaefe8f03537600ec31898b506e3a85ce79b94f26fb6cc1920c9e18eb";
+  virtualboxSha256 = "06db4060caadc70346335c0a731ca6667cdabf206de289c64f3f96f2d341b9d0";
 
   kvmPatchVboxVersion = "7.2.6";
   kvmPatchVersion = "20260201";
diff --git a/pkgs/applications/virtualization/virtualbox/extpack.nix b/pkgs/applications/virtualization/virtualbox/extpack.nix
index f4cc780b954b..effed196042b 100644
--- a/pkgs/applications/virtualization/virtualbox/extpack.nix
+++ b/pkgs/applications/virtualization/virtualbox/extpack.nix
@@ -5,7 +5,7 @@
 }:
 fetchurl rec {
   pname = "virtualbox-extpack";
-  version = "7.2.16";
+  version = "7.2.18";
   name = "Oracle_VirtualBox_Extension_Pack-${version}.vbox-extpack";
   url = "https://download.virtualbox.org/virtualbox/${version}/${name}";
   sha256 =
@@ -13,7 +13,7 @@ fetchurl rec {
     # Thus do not use `nix-prefetch-url` but instead plain old `sha256sum`.
     # Checksums can also be found at https://download.virtualbox.org/virtualbox/${version}/SHA256SUMS
     let
-      value = "d1e268cfa05223fd651703043af09f39dfb90da259ce9ec093d9d9b022f19689";
+      value = "e06834239947db06cc077d464bbb15d6441917ca03573e518506344dc28b64b9";
     in
     assert (builtins.stringLength value) == 64;
     value;
diff --git a/pkgs/applications/virtualization/virtualbox/guest-additions-iso/default.nix b/pkgs/applications/virtualization/virtualbox/guest-additions-iso/default.nix
index 0de81245bc84..372d956d057c 100644
--- a/pkgs/applications/virtualization/virtualbox/guest-additions-iso/default.nix
+++ b/pkgs/applications/virtualization/virtualbox/guest-additions-iso/default.nix
@@ -5,7 +5,7 @@
 }:
 fetchurl {
   url = "http://download.virtualbox.org/virtualbox/${virtualboxVersion}/VBoxGuestAdditions_${virtualboxVersion}.iso";
-  sha256 = "c9349c0231d81c821fc1de7b9592bf07bb7c3f111c3f942ddddc211496ef7a3e";
+  sha256 = "346ea2b9ed47bb954464af83835b14bd8afa5fc1864f34e2561ed923fb74981c";
   meta = {
     description = "Guest additions ISO for VirtualBox";
     longDescription = ''
diff --git a/pkgs/applications/virtualization/virtualbox/guest-additions/default.nix b/pkgs/applications/virtualization/virtualbox/guest-additions/default.nix
index 693fbde5b93f..60a5f2b0c454 100644
--- a/pkgs/applications/virtualization/virtualbox/guest-additions/default.nix
+++ b/pkgs/applications/virtualization/virtualbox/guest-additions/default.nix
@@ -18,9 +18,9 @@
   libx11,
 }:
 let
-  virtualboxVersion = "7.2.16";
+  virtualboxVersion = "7.2.18";
   virtualboxSubVersion = "";
-  virtualboxSha256 = "50356ccdaefe8f03537600ec31898b506e3a85ce79b94f26fb6cc1920c9e18eb";
+  virtualboxSha256 = "06db4060caadc70346335c0a731ca6667cdabf206de289c64f3f96f2d341b9d0";
 
   platform =
     if stdenv.hostPlatform.isAarch64 then
@@ -98,7 +98,9 @@ stdenv.mkDerivation {
 
   # https://github.com/VirtualBox/virtualbox/issues/812
   postPatch = ''
-    substituteInPlace ./src/vboxguest-${virtualboxVersion}_NixOS/vboxvideo/vbox_fb.c --replace-fail "RTLNX_VER_MIN(6,19,0)" "RTLNX_VER_RANGE(6,6,152, 6,6,999) || RTLNX_VER_RANGE(6,12,103, 6,12,999) || RTLNX_VER_RANGE(6,18,44, 6,18,999) || RTLNX_VER_MIN(6,19,0)"
+    substituteInPlace ./src/vboxguest-${virtualboxVersion}_NixOS/vboxvideo/vbox_fb.c \
+      --replace-fail "RTLNX_VER_MIN(6,19,0) || RTLNX_VER_RANGE(6,12,103, 6,13,0)" \
+      "RTLNX_VER_MIN(6,19,0) || RTLNX_VER_RANGE(6,12,103, 6,13,0) || RTLNX_VER_RANGE(6,6,152, 6,6,999) || RTLNX_VER_RANGE(6,18,44, 6,18,999)"
   '';
 
   buildPhase = ''
diff --git a/pkgs/by-name/be/bedtools/package.nix b/pkgs/by-name/be/bedtools/package.nix
index 6997af241be2..84a19a5ce3bd 100644
--- a/pkgs/by-name/be/bedtools/package.nix
+++ b/pkgs/by-name/be/bedtools/package.nix
@@ -6,21 +6,23 @@
   python3,
   bzip2,
   xz,
+  versionCheckHook,
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation (finalAttrs: {
   pname = "bedtools";
   version = "2.31.1";
 
+  __structuredAttrs = true;
+  strictDeps = true;
+
   src = fetchFromGitHub {
     owner = "arq5x";
     repo = "bedtools2";
-    rev = "v${version}";
-    sha256 = "sha256-rrk+FSv1bGL0D1lrIOsQu2AT7cw2T4lkDiCnzil5fpg=";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-rrk+FSv1bGL0D1lrIOsQu2AT7cw2T4lkDiCnzil5fpg=";
   };
 
-  strictDeps = true;
-
   nativeBuildInputs = [
     python3
   ];
@@ -31,16 +33,28 @@ stdenv.mkDerivation rec {
     xz
   ];
 
-  cxx = if stdenv.cc.isClang then "clang++" else "g++";
-  cc = if stdenv.cc.isClang then "clang" else "gcc";
-  buildPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cxx} CC=${cc} -j $NIX_BUILD_CORES";
-  installPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cxx} CC=${cc} install";
+  enableParallelBuilding = true;
+
+  makeFlags = [
+    "prefix=${placeholder "out"}"
+    # The Makefiles hardcode `CC = gcc` and `CXX = g++`.
+    "CC=${stdenv.cc.targetPrefix}cc"
+    "CXX=${stdenv.cc.targetPrefix}c++"
+  ];
+
+  nativeInstallCheckInputs = [
+    versionCheckHook
+  ];
+  doInstallCheck = true;
 
   meta = {
     description = "Powerful toolset for genome arithmetic";
-    license = lib.licenses.gpl2;
     homepage = "https://bedtools.readthedocs.io/en/latest/";
+    downloadPage = "https://github.com/arq5x/bedtools2";
+    changelog = "https://github.com/arq5x/bedtools2/releases/tag/${finalAttrs.src.tag}";
+    license = lib.licenses.mit;
+    mainProgram = "bedtools";
     maintainers = with lib.maintainers; [ jbedo ];
     platforms = lib.platforms.unix;
   };
-}
+})
diff --git a/pkgs/by-name/ca/cargo-risczero/package.nix b/pkgs/by-name/ca/cargo-risczero/package.nix
index 96ba444423d6..6b815bf4f579 100644
--- a/pkgs/by-name/ca/cargo-risczero/package.nix
+++ b/pkgs/by-name/ca/cargo-risczero/package.nix
@@ -6,6 +6,7 @@
   pkg-config,
   openssl,
   nix-update-script,
+  stdenv, # for meta.broken
 }:
 let
   # That is from cargoDeps/risc0-circuit-recursion/build.rs
@@ -44,6 +45,8 @@ rustPlatform.buildRustPackage (finalAttrs: {
   passthru.updateScript = nix-update-script { };
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "Cargo extension to help create, manage, and test RISC Zero projects";
     mainProgram = "cargo-risczero";
     homepage = "https://risczero.com";
diff --git a/pkgs/by-name/ca/cargo-ui/package.nix b/pkgs/by-name/ca/cargo-ui/package.nix
index c39fc868fd0a..0189818ba82d 100644
--- a/pkgs/by-name/ca/cargo-ui/package.nix
+++ b/pkgs/by-name/ca/cargo-ui/package.nix
@@ -61,6 +61,8 @@ rustPlatform.buildRustPackage (finalAttrs: {
   };
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "GUI for Cargo";
     mainProgram = "cargo-ui";
     homepage = "https://github.com/slint-ui/cargo-ui";
diff --git a/pkgs/by-name/cl/claude-agent-acp/package.nix b/pkgs/by-name/cl/claude-agent-acp/package.nix
index e1888698ce14..b2ce705bf89f 100644
--- a/pkgs/by-name/cl/claude-agent-acp/package.nix
+++ b/pkgs/by-name/cl/claude-agent-acp/package.nix
@@ -8,16 +8,16 @@
 
 buildNpmPackage (finalAttrs: {
   pname = "claude-agent-acp";
-  version = "0.75.1";
+  version = "0.79.0";
 
   src = fetchFromGitHub {
     owner = "agentclientprotocol";
     repo = "claude-agent-acp";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-LEubm7Ck22olYsP+l9tis9Qcw77fpy7gBT42P/Aj+KY=";
+    hash = "sha256-Xezx6CM44czWrfJ/1LyJkMXV33ufIfYKtNL7qeQCths=";
   };
 
-  npmDepsHash = "sha256-78vx17sJlklHPq98gZxgQFB6BFGp0uGrcpj7tv978qg=";
+  npmDepsHash = "sha256-d0UpoVGVC3q0jhgOAvGLqxul1J8ZO1bTwXprWg+FKc4=";
 
   nativeBuildInputs = [ makeWrapper ];
 
diff --git a/pkgs/by-name/cl/clfft/package.nix b/pkgs/by-name/cl/clfft/package.nix
index df0b9f0fd36d..4a8904872c56 100644
--- a/pkgs/by-name/cl/clfft/package.nix
+++ b/pkgs/by-name/cl/clfft/package.nix
@@ -52,6 +52,8 @@ stdenv.mkDerivation (finalAttrs: {
   env.CXXFLAGS = "-std=c++98";
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "Library containing FFT functions written in OpenCL";
     longDescription = ''
       clFFT is a software library containing FFT functions written in OpenCL.
diff --git a/pkgs/by-name/co/colmap/package.nix b/pkgs/by-name/co/colmap/package.nix
index a7b98f1396b6..32ea1b0886e2 100644
--- a/pkgs/by-name/co/colmap/package.nix
+++ b/pkgs/by-name/co/colmap/package.nix
@@ -191,6 +191,11 @@ stdenv'.mkDerivation (finalAttrs: {
         "*GPU*"
         "*OpenGL*"
       ]
+      ++ lib.optionals stdenv'.hostPlatform.isAarch64 [
+        # least_absolute_deviations_test.cc:311: Failure
+        # Value of: solver.Valid(), Actual: true, Expected: false
+        "*ParameterizedLeastAbsoluteDeviationsTests.RidgeRegularization/0"
+      ]
       ++ lib.optionals stdenv'.hostPlatform.isDarwin [
         # reconstruction_pruning_test.cc:65: Failure
         # Expected: (redundant_point3D_ids.size()) > (prev_num_redundant_points3D), actual: 0 vs 0
diff --git a/pkgs/by-name/co/comaps/package.nix b/pkgs/by-name/co/comaps/package.nix
index c9f84ff47d06..151d30630f3e 100644
--- a/pkgs/by-name/co/comaps/package.nix
+++ b/pkgs/by-name/co/comaps/package.nix
@@ -38,18 +38,18 @@ let
 
   # Update mapRev based on v field and mapSeries near the top in https://codeberg.org/comaps/comaps/src/branch/main/data/countries.txt
   mapSeries = "2026.06.28";
-  mapRev = 260714;
+  mapRev = 260830;
 
   worldMap = fetchurl {
     name = "World-${mapSeries}-${toString mapRev}.mwm";
     url = "https://mapgen-fi-1.comaps.app/maps/${mapSeries}/${toString mapRev}/World.mwm";
-    hash = "sha256-+EttNsix+9bB0/eOsPaxtZEfPDqQrj8qfZg2qDaLFVc=";
+    hash = "sha256-TcaGJK8xAkceA7wFsCrYt6euOnts0w7LZCKLFPnU3wM=";
   };
 
   worldCoasts = fetchurl {
     name = "WorldCoasts-${mapSeries}-${toString mapRev}.mwm";
     url = "https://mapgen-fi-1.comaps.app/maps/${mapSeries}/${toString mapRev}/WorldCoasts.mwm";
-    hash = "sha256-MsXFqnoyQQTTJR1f8ihiqzCYuuRAVbRpoXfPPkVFa1E=";
+    hash = "sha256-pNb0cLGRN6YkliraL+DZyAPh+JJSM6vTzoejeKvi/oc=";
   };
 
   pythonEnv = python3.withPackages (
@@ -60,7 +60,7 @@ let
 in
 stdenv.mkDerivation (finalAttrs: {
   pname = "comaps";
-  version = "2026.08.07-3";
+  version = "2026.08.31-14";
 
   strictDeps = true;
   __structuredAttrs = true;
@@ -69,7 +69,7 @@ stdenv.mkDerivation (finalAttrs: {
     owner = "comaps";
     repo = "comaps";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-ft7VYIMdg8IOl4gfm7Zg5EQjli0YDGuepwP1X9w2Sos=";
+    hash = "sha256-mnLvDuXCi7guw0vU3TnqmvvgB1l7mN/AKwtF/79LGd4=";
     fetchSubmodules = true;
   };
 
diff --git a/pkgs/by-name/de/deploy-rs/package.nix b/pkgs/by-name/de/deploy-rs/package.nix
index 8350d36f8650..0b1d3b22ae8d 100644
--- a/pkgs/by-name/de/deploy-rs/package.nix
+++ b/pkgs/by-name/de/deploy-rs/package.nix
@@ -2,20 +2,28 @@
   lib,
   fetchFromGitHub,
   rustPlatform,
+  nix-update-script,
 }:
 
 rustPlatform.buildRustPackage {
   pname = "deploy-rs";
-  version = "0-unstable-2026-02-02";
+  version = "0-unstable-2026-09-14";
 
   src = fetchFromGitHub {
     owner = "serokell";
     repo = "deploy-rs";
-    rev = "77c906c0ba56aabdbc72041bf9111b565cdd6171";
-    hash = "sha256-hwsYgDnby50JNVpTRYlF3UR/Rrpt01OrxVuryF40CFY=";
+    rev = "e760371d631165e7d8de5b0dcf148e21ec4c16f0";
+    hash = "sha256-UXFQ7tFiwn8sPz0EV4CBB2PCf/ZiGIHWn/6MXk81Lxs=";
   };
 
-  cargoHash = "sha256-9O93YTEz+e2oxenE0gwxsbz55clbKo9+37yVOqz7ErE=";
+  cargoHash = "sha256-ONGMdmkKGPJ+6KF2hkZQBefkug/C5ZEqPidKR6OkCbU=";
+
+  # Tests use the FSEvents API on macOS, which the darwin sandbox blocks by default
+  sandboxProfile = ''
+    (allow mach-lookup (global-name "com.apple.FSEvents"))
+  '';
+
+  passthru.updateScript = nix-update-script { extraArgs = [ "--version=branch" ]; };
 
   meta = {
     description = "Multi-profile Nix-flake deploy tool";
diff --git a/pkgs/by-name/de/descent3-unwrapped/package.nix b/pkgs/by-name/de/descent3-unwrapped/package.nix
index 124a437fd806..992606c3a7ef 100644
--- a/pkgs/by-name/de/descent3-unwrapped/package.nix
+++ b/pkgs/by-name/de/descent3-unwrapped/package.nix
@@ -20,11 +20,11 @@ stdenv.mkDerivation rec {
   # the wrapped version of Descent 3. Once there’s a stable version of Descent
   # 3 that supports the -additionaldir command-line option, we can stop using
   # an unstable version of Descent 3.
-  version = "1.5.0-beta-unstable-2026-01-21";
+  version = "1.5.0-beta-unstable-2026-09-16";
   src = fetchFromGitHub {
     owner = "DescentDevelopers";
     repo = "Descent3";
-    rev = "156cba8aafd997d27deb0902ba6026bcdcc1cfaf";
+    rev = "a3e82bc292dab95afd2bf3dc0988c065e041b3ef";
     leaveDotGit = true;
     # Descent 3 is supposed to display its Git commit hash in the bottom right
     # corner of the main menu. That feature only works if either the .git
@@ -50,7 +50,7 @@ stdenv.mkDerivation rec {
       git rev-parse --verify HEAD | tr --delete '\n' > git-hash.txt
       rm -r .git
     '';
-    hash = "sha256-NsZPGgIzI2mE3mJ7eoczaNDkGZUpMUMBRLK2qt2WPgk=";
+    hash = "sha256-yS2tjVNtUEbsMbdt21TK7VqN3rm66BxNxI/GNcAHCIA=";
   };
 
   hardeningDisable = [ "format" ];
diff --git a/pkgs/by-name/di/dico/package.nix b/pkgs/by-name/di/dico/package.nix
index 6032f5892120..2de8c334e7b2 100644
--- a/pkgs/by-name/di/dico/package.nix
+++ b/pkgs/by-name/di/dico/package.nix
@@ -47,6 +47,8 @@ stdenv.mkDerivation (finalAttrs: {
   doCheck = !stdenv.hostPlatform.isDarwin;
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "Flexible dictionary server and client implementing RFC 2229";
     homepage = "https://www.gnu.org/software/dico/";
     license = lib.licenses.gpl3Plus;
diff --git a/pkgs/by-name/fo/forgejo/lts.nix b/pkgs/by-name/fo/forgejo/lts.nix
index cab0bde6ee10..9170fb732625 100644
--- a/pkgs/by-name/fo/forgejo/lts.nix
+++ b/pkgs/by-name/fo/forgejo/lts.nix
@@ -1,8 +1,8 @@
 import ./generic.nix {
-  version = "15.0.8";
-  hash = "sha256-tpgqa6RvQ/xesSv/THjlXiM0JQqzgMQJiuUAOFrgGpo=";
+  version = "15.0.9";
+  hash = "sha256-6EtUVoB8/PsgbWiB4j9hLYOYyjPKCykzILWezDpJnAs=";
   npmDepsHash = "sha256-g3ebO2W8lnHeS6T6bMJkC/UVDA3pa5O5v64QJG5irn0=";
-  vendorHash = "sha256-p9U/nvAHSC2Pj09gfDWQVKl+1TKB0PTqW2E+gKZ4/D4=";
+  vendorHash = "sha256-KW0WIfRm53pVOiWOYoSQaCz7BO+lFykAQdgdgXesXkY=";
   lts = true;
   nixUpdateExtraArgs = [
     "--override-filename"
diff --git a/pkgs/by-name/fo/forgejo/package.nix b/pkgs/by-name/fo/forgejo/package.nix
index 2a24f6df7c4c..a74543ffc008 100644
--- a/pkgs/by-name/fo/forgejo/package.nix
+++ b/pkgs/by-name/fo/forgejo/package.nix
@@ -1,8 +1,8 @@
 import ./generic.nix {
-  version = "16.0.4";
-  hash = "sha256-oEw8FdJuTfxjMaVxQqbpAIWCYDhxPvifZv8UfqeHbRs=";
-  npmDepsHash = "sha256-QwZ8X0pVxs5u4jMOqy3VGcBGVqqDKpLCMPmwoECVwEg=";
-  vendorHash = "sha256-GRh9jh7x4xP8MPEEWG0BxKAXtTz3wjueIcPtbkksgqY=";
+  version = "16.0.5";
+  hash = "sha256-Ci6QuRNZ4miUzqPz5/YPQgo/wbndN3vFsBigApW8XOY=";
+  npmDepsHash = "sha256-CMShFS5JOqVwjLf1VKRaRD04GLuL4kRti27pVe4Pe2k=";
+  vendorHash = "sha256-yI74OphRoUvnsQ9qfnQdpUg2Jj4j72zVzP/Jr10XUWM=";
   lts = false;
   nixUpdateExtraArgs = [
     "--override-filename"
diff --git a/pkgs/by-name/gi/git-chain/package.nix b/pkgs/by-name/gi/git-chain/package.nix
index 1162c5794346..41faff0a2aa4 100644
--- a/pkgs/by-name/gi/git-chain/package.nix
+++ b/pkgs/by-name/gi/git-chain/package.nix
@@ -6,6 +6,7 @@
   openssl,
   git,
   nix-update-script,
+  stdenv, # for meta.broken
 }:
 
 rustPlatform.buildRustPackage {
@@ -30,6 +31,8 @@ rustPlatform.buildRustPackage {
   passthru.updateScript = nix-update-script { extraArgs = [ "--version=branch" ]; };
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "Tool for rebasing a chain of local git branches";
     homepage = "https://github.com/dashed/git-chain";
     license = lib.licenses.mit;
diff --git a/pkgs/by-name/gi/git-together/package.nix b/pkgs/by-name/gi/git-together/package.nix
index 4c7ffd68a8a9..f5707f6ea1c8 100644
--- a/pkgs/by-name/gi/git-together/package.nix
+++ b/pkgs/by-name/gi/git-together/package.nix
@@ -4,6 +4,7 @@
   rustPlatform,
   openssl,
   pkg-config,
+  stdenv, # for meta.broken
 }:
 
 rustPlatform.buildRustPackage (finalAttrs: {
@@ -25,6 +26,8 @@ rustPlatform.buildRustPackage (finalAttrs: {
   cargoHash = "sha256-5LKKjHzIlXw0bUmF7GDCVW0cptCxohq6CNPIrMZKorM=";
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     changelog = "https://github.com/kejadlen/git-together/releases/tag/v${finalAttrs.version}";
     description = "Better commit attribution while pairing without messing with your git workflow";
     homepage = "https://github.com/kejadlen/git-together";
diff --git a/pkgs/by-name/go/goperf/package.nix b/pkgs/by-name/go/goperf/package.nix
index be6561f001ea..055e2bad1b54 100644
--- a/pkgs/by-name/go/goperf/package.nix
+++ b/pkgs/by-name/go/goperf/package.nix
@@ -9,15 +9,15 @@
 
 buildGoModule (finalAttrs: {
   pname = "goperf";
-  version = "0-unstable-2026-08-13";
+  version = "0-unstable-2026-09-08";
 
   src = fetchgit {
     url = "https://go.googlesource.com/perf";
-    rev = "fd4a688df89207abdabe0a0cf5b2cd9ccfd376d2";
-    hash = "sha256-YgMIIF9DAjyAPpZJtVoOKSatNhRPg/nPOYr0P06Fi5s=";
+    rev = "22c9c6c9d4da6248aedbc79f02ecedcd59f8f5f2";
+    hash = "sha256-RSiI5I92l9bMWxTbHNKhcti4OKj8kD9yFxeHaWQJiFU=";
   };
 
-  vendorHash = "sha256-AZx9tPzsPvjc5kpmiBa6eYKtrw0hczYi0sbcd/lkiiA=";
+  vendorHash = "sha256-9y6O/R2fOPYAGjlIZ2lcO1TNiZPj6My3EoPRiiFZu3U=";
 
   passthru.updateScript = writeShellScript "update-goperf" ''
     export UPDATE_NIX_ATTR_PATH=goperf
diff --git a/pkgs/by-name/gs/gsender/package.nix b/pkgs/by-name/gs/gsender/package.nix
index d78939d9616f..180d7f92d393 100644
--- a/pkgs/by-name/gs/gsender/package.nix
+++ b/pkgs/by-name/gs/gsender/package.nix
@@ -5,12 +5,12 @@
 }:
 
 let
-  version = "1.6.3";
+  version = "1.6.4";
   pname = "gsender";
 
   src = fetchurl {
     url = "https://github.com/Sienci-Labs/gsender/releases/download/v${version}/gSender-${version}-Linux-Intel-64Bit.AppImage";
-    hash = "sha256-xWsRSzJm5aA13qCBI2MRzauvPqoOBtxqtGb3gLAa3sI=";
+    hash = "sha256-N8jAy5+2UPC7trtUF7kVztDA3aiFyHEAcyfcCobIRe4=";
   };
 
   appimageContents = appimageTools.extract { inherit pname version src; };
diff --git a/pkgs/by-name/ha/handlr-regex/package.nix b/pkgs/by-name/ha/handlr-regex/package.nix
index 5437382a2ccd..f186bd15b8d9 100644
--- a/pkgs/by-name/ha/handlr-regex/package.nix
+++ b/pkgs/by-name/ha/handlr-regex/package.nix
@@ -45,6 +45,8 @@ rustPlatform.buildRustPackage (finalAttrs: {
   passthru.updateScript = nix-update-script { };
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "Fork of handlr with support for regex";
     homepage = "https://github.com/Anomalocaridid/handlr-regex";
     license = lib.licenses.mit;
diff --git a/pkgs/by-name/ho/homepage-dashboard/package.nix b/pkgs/by-name/ho/homepage-dashboard/package.nix
index 84d988c3d630..d14e9c9a624a 100644
--- a/pkgs/by-name/ho/homepage-dashboard/package.nix
+++ b/pkgs/by-name/ho/homepage-dashboard/package.nix
@@ -31,13 +31,13 @@ let
 in
 stdenv.mkDerivation (finalAttrs: {
   pname = "homepage-dashboard";
-  version = "2.2.0";
+  version = "2.3.0";
 
   src = fetchFromGitHub {
     owner = "gethomepage";
     repo = "homepage";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-dAgOUOM97I8iAFIKtQC2ziMPy7ZUE3xvvLbPvwPhSdc=";
+    hash = "sha256-a5BK9ekt78tnfxQRpij+CXJz48MztJNQVKM57NfIX+0=";
   };
 
   pnpmDeps = fetchPnpmDeps {
diff --git a/pkgs/by-name/le/lean/package.nix b/pkgs/by-name/le/lean/package.nix
index e71f25725990..7311994456a5 100644
--- a/pkgs/by-name/le/lean/package.nix
+++ b/pkgs/by-name/le/lean/package.nix
@@ -68,6 +68,8 @@ stdenv.mkDerivation rec {
   '';
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "Automatic and interactive theorem prover";
     homepage = "https://leanprover.github.io/";
     changelog = "https://github.com/leanprover-community/lean/blob/v${version}/doc/changes.md";
diff --git a/pkgs/by-name/li/liblbfgs/package.nix b/pkgs/by-name/li/liblbfgs/package.nix
index d4c1a065d958..2acd91f99b9d 100644
--- a/pkgs/by-name/li/liblbfgs/package.nix
+++ b/pkgs/by-name/li/liblbfgs/package.nix
@@ -14,7 +14,9 @@ stdenv.mkDerivation (finalAttrs: {
   };
 
   meta = {
-    broken = (stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64);
+    # last successful hydra build on darwin was in 2024
+    broken =
+      (stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64) || stdenv.hostPlatform.isDarwin;
     description = "Library of Limited-memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS)";
     homepage = "http://www.chokkan.org/software/liblbfgs/";
     license = lib.licenses.mit;
diff --git a/pkgs/by-name/li/librewolf-unwrapped/librewolf.nix b/pkgs/by-name/li/librewolf-unwrapped/librewolf.nix
index a58fb3f9303a..86773237b7c7 100644
--- a/pkgs/by-name/li/librewolf-unwrapped/librewolf.nix
+++ b/pkgs/by-name/li/librewolf-unwrapped/librewolf.nix
@@ -45,6 +45,8 @@ rec {
     cp ${source}/assets/search-config-icons.json services/settings/dumps/main/search-config-icons.json
     cp ${source}/assets/2c4b8834-030c-4097-a887-c7506689095c services/settings/dumps/main/search-config-icons
     cp ${source}/assets/2c4b8834-030c-4097-a887-c7506689095c.meta.json services/settings/dumps/main/search-config-icons
+    cp ${source}/assets/marsigner.der toolkit/mozapps/update/updater/release_primary.der
+    cp ${source}/assets/marsigner2.der toolkit/mozapps/update/updater/release_secondary.der
     sed -i '/MOZ_SERVICES_HEALTHREPORT/ s/True/False/' browser/moz.configure
 
     cp ${source}/patches/pref-pane/category-librewolf.svg browser/themes/shared/preferences
@@ -53,9 +55,8 @@ rec {
     cp ${source}/patches/pref-pane/librewolf.js browser/components/preferences
 
     # override firefox version
-    for fn in browser/config/version.txt browser/config/version_display.txt; do
-      echo "${packageVersion}" > "$fn"
-    done
+    echo "${firefox.version}" > browser/config/version.txt
+    echo "${packageVersion}" > browser/config/version_display.txt
 
     echo "patching appstrings.properties"
     find . -path '*/appstrings.properties' -exec sed -i s/Firefox/LibreWolf/ {} \;
diff --git a/pkgs/by-name/li/librewolf-unwrapped/src.json b/pkgs/by-name/li/librewolf-unwrapped/src.json
index 5885fcd34d29..786552fc210a 100644
--- a/pkgs/by-name/li/librewolf-unwrapped/src.json
+++ b/pkgs/by-name/li/librewolf-unwrapped/src.json
@@ -1,11 +1,11 @@
 {
-  "packageVersion": "155.0.1-1",
+  "packageVersion": "156.0-1",
   "source": {
-    "rev": "155.0.1-1",
-    "hash": "sha256-UjGUEDRohgDcNYUnX7EhNvDRPHUcYuC3GsNOpJ3yYFw="
+    "rev": "156.0-1",
+    "hash": "sha256-r5i+lFRxx5pcMcDotl9gIEuRytqyY0/opAYTcljUF4c="
   },
   "firefox": {
-    "version": "155.0.1",
-    "hash": "sha512-bRN6ejFcsdCqwaP+MUr4D+KQxJt8Lkf4aHsl1HIJJ7Kg3HGj2p119sq0eQZ9sRTKpnMtF+iIsKv86ZI4qK8POQ=="
+    "version": "156.0",
+    "hash": "sha512-BGMwSgiYZw0kgRT2b3wjUWauI5fDmJp8h4yW8MWJ+7uh8ch0MtqiJjO5+t2UOUrfHcN/DmfSKwZsde/l7q11zg=="
   }
 }
diff --git a/pkgs/by-name/li/lighthouse-steamvr/package.nix b/pkgs/by-name/li/lighthouse-steamvr/package.nix
index 6f40846fb7d2..6f95f9df79d0 100644
--- a/pkgs/by-name/li/lighthouse-steamvr/package.nix
+++ b/pkgs/by-name/li/lighthouse-steamvr/package.nix
@@ -8,16 +8,16 @@
 
 rustPlatform.buildRustPackage (finalAttrs: {
   pname = "Lighthouse";
-  version = "2.0.0";
+  version = "2.1.0";
 
   src = fetchFromGitHub {
     owner = "ShayBox";
     repo = "Lighthouse";
     rev = finalAttrs.version;
-    hash = "sha256-c3AEoNpuPqCn37WIDVbJDX61qM6Pg/f6sMro3M/skNc=";
+    hash = "sha256-TCl3X1AmJx53Dr0A9DYbk0HkaDjW0dgD4Jssg7W4vFk=";
   };
 
-  cargoHash = "sha256-Kow/M7FDgaZiLcWU9se5ut3lrVOtAZebQTgURzSORsA=";
+  cargoHash = "sha256-1xl8X0JQbeGlM5wMdTpFQsZ2lLPndOZSU57zVc6rhe8=";
 
   nativeBuildInputs = [ pkg-config ];
 
diff --git a/pkgs/by-name/lo/loki/package.nix b/pkgs/by-name/lo/loki/package.nix
index 54bf660d9e2f..349217f6bfcd 100644
--- a/pkgs/by-name/lo/loki/package.nix
+++ b/pkgs/by-name/lo/loki/package.nix
@@ -25,6 +25,8 @@ stdenv.mkDerivation (finalAttrs: {
   enableParallelBuilding = true;
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "C++ library of designs, containing flexible implementations of common design patterns and idioms";
     homepage = "https://loki-lib.sourceforge.net";
     license = lib.licenses.mit;
diff --git a/pkgs/by-name/lu/luarocks-packages-updater/updater.py b/pkgs/by-name/lu/luarocks-packages-updater/updater.py
index 1c59ee4e2171..76d2a760ce90 100755
--- a/pkgs/by-name/lu/luarocks-packages-updater/updater.py
+++ b/pkgs/by-name/lu/luarocks-packages-updater/updater.py
@@ -260,6 +260,8 @@ class LuaEditor(nixpkgs_plugin_update.Editor):
             )
             f.write(header2)
             for plugin, nix_expr in results:
+                # Preserved packages also need canonical license metadata.
+                nix_expr = normalize_license_metadata(nix_expr)
                 f.write(f"  {plugin.normalized_name} = {nix_expr}")
             f.write(FOOTER)
             f.flush()
diff --git a/pkgs/by-name/mi/mindustry/deps.json b/pkgs/by-name/mi/mindustry/deps.json
index d0782d4a749b..c6add651a088 100644
--- a/pkgs/by-name/mi/mindustry/deps.json
+++ b/pkgs/by-name/mi/mindustry/deps.json
@@ -2,10 +2,10 @@
  "!comment": "This is a nixpkgs Gradle dependency lockfile. For more details, refer to the Gradle section in the nixpkgs manual.",
  "!version": 1,
  "https://jitpack.io/com/github": {
-  "Anuken#rhino/e74ac129d2bff72c1deb536d7d99a0dbb7046d2e": {
-   "jar": "sha256-iRvhgKzqoi/8VMmkiM5ibGULv6e07A98e8QoMB6XROQ=",
-   "module": "sha256-c02sDzu5Z+dMXP2DcCFen9ImCWTtZ2I06uSrrtJ8QIo=",
-   "pom": "sha256-kUrWd9wtr/SN21fjmyInwRN8CSxp2nKfeji3qz1OteA="
+  "Anuken#rhino/32395f942976a6d1d21ec9877664554cd5762306": {
+   "jar": "sha256-FLi9abGTI+nP6mStbPgvue7fXIgUrKqN9EZZ4YHj6rE=",
+   "module": "sha256-4OnGk4UsPE50E7Q9V9suDCsm0RF0SWFNKJoPSPU9r2c=",
+   "pom": "sha256-UukU923dR7GWImrL4fdRbVD/rIci4YvxFNTdSZ35NP4="
   },
   "Anuken#steamworks4j/da41c05b7a2a44c8625ca0ba7d6ca1a2e73f621a": {
    "jar": "sha256-+8oDVVVbQSpioDAUXKm+vqe3YutsioD4eON7bp9JW0k=",
@@ -53,25 +53,25 @@
   "ch/qos/logback#logback-parent/1.4.14": {
    "pom": "sha256-5bddPe8EJ1dkUEoXp8GqHj7jcKWxpUiIS74Vfr3eXv0="
   },
-  "com/badlogicgames/jnigen#jnigen-commons/3.1.1": {
-   "jar": "sha256-GhpDx0Kwd5H1I6LjAGzkysOnyWC60i3qcE0lf5+5Uic=",
-   "module": "sha256-h5TNmSGiisv/kGGm6e7jU3JW26POyMo58eKt7d1zG2E=",
-   "pom": "sha256-lKy0mhhj7cQgfVn6iwc9U1m4PuGhX+eYY0RTlYvaoTQ="
+  "com/badlogicgames/jnigen#jnigen-commons/3.1.2": {
+   "jar": "sha256-DnSM9SIMqQeWvz61JeOohIFW/zC2JB8g/NrozSoY/I0=",
+   "module": "sha256-0XfylGOzkNPCvzxbG0Vm446uZsMr2yu5DX7PraM1TPM=",
+   "pom": "sha256-wsncZ0SMwzKXNVcykrnyA0TYcQXTwpfU9oPC7W/9QhU="
   },
-  "com/badlogicgames/jnigen#jnigen-core/3.1.1": {
-   "jar": "sha256-9sl8HgFko1FKWFPR7+emTKYoXAZis5C6GGEMVRddqOM=",
-   "module": "sha256-arm2LaOD7BF6rY5Iv4bW2e3SP5Gq6TgJhlrO9vkg+AY=",
-   "pom": "sha256-ig4v9L0DMgIIumfHwy+YZbn3dKwvz97+nPdHHT2oOl4="
+  "com/badlogicgames/jnigen#jnigen-core/3.1.2": {
+   "jar": "sha256-qWsuGL/3szIep6tUkgtrsr75NnDqN0MeFbuwXXYtpbU=",
+   "module": "sha256-g/a46oN3csFoVsvvkF72dbtSNIRvJSTfqt8TMJa/7/A=",
+   "pom": "sha256-2QcHJnrte5dI8W5j5/TleEIxQNI7eLtFm1jkJh5r26w="
   },
-  "com/badlogicgames/jnigen#jnigen-generator/3.1.1": {
-   "jar": "sha256-ipB6ZfxDED5WNDk7eq8Cc6Iog9AgkoBbyCGrmvMht4E=",
-   "module": "sha256-l4Y/xRC2r16qspcGcADJsnp2nY2owo56r+SVGEXyc/U=",
-   "pom": "sha256-/MiUlSd0enOtc7FBjbjjVlW/tfTaIF+GjuEq0rmbQlg="
+  "com/badlogicgames/jnigen#jnigen-generator/3.1.2": {
+   "jar": "sha256-T1ThobVCn/xtPvHuLLdSMKhNcwjLopmtRXASgexW4bo=",
+   "module": "sha256-va5brIvJXoPt0xlONHNCJW9xOOLrmRNcjasfcCvrjrA=",
+   "pom": "sha256-tuAk/T9yUIJ0Ue4jjWnXEVY/nrZk4u9RTZqEXugSKgE="
   },
-  "com/badlogicgames/jnigen#jnigen-gradle/3.1.1": {
-   "jar": "sha256-riahTjGeDivvNIIZdnd6hZ8L0a0omdLioDJ4VT6PXEw=",
-   "module": "sha256-Smwq0R4Dlv2f5RdgwERw18Zps62iGewN5bttg6pY8pg=",
-   "pom": "sha256-Yh5nfY9xbZWvlhWI1UFOWJud0YG/KEl7LR75XVf/mV8="
+  "com/badlogicgames/jnigen#jnigen-gradle/3.1.2": {
+   "jar": "sha256-WhpECjrL4ygWsucudyEq/h7sTLWQVsPnn5tPNg9dY1I=",
+   "module": "sha256-8e5D0+ciQ7hiB30I6eOne0g0/plo6m2ug4bFp6Y0Ppo=",
+   "pom": "sha256-OyjiQiUnQdwrmuaIIDg+KMcYyoNbUC7Ohp173HKWOEQ="
   },
   "com/github/javaparser#javaparser-core/3.14.14": {
    "pom": "sha256-70ERyN/Uh+Zp5w1Qzz2z8O3YuTLKvjXmYzuzzuuGpIo="
@@ -80,12 +80,19 @@
    "jar": "sha256-okxPp3mf/gx6mvEdTuzXVwmO1EmPhgZ78otGsr/qGDM=",
    "pom": "sha256-ZiXjSXeLPDEAJopgk6v0RHLl6WYe85nDNHjYdx+Fgu0="
   },
+  "com/github/javaparser#javaparser-core/3.28.2": {
+   "jar": "sha256-tUmaOxxAsWwGcfq+R4yar+qzgWDG/edKbBP0LYZxbs0=",
+   "pom": "sha256-h9KzM9/sloltWknoCpW5LvVy9hDoSCdrReqgYeBbQTI="
+  },
   "com/github/javaparser#javaparser-parent/3.14.14": {
    "pom": "sha256-RwgtW3eLzkmjEnRtUWHJ48yhfYwh2eO+MTF68Io2FDc="
   },
   "com/github/javaparser#javaparser-parent/3.26.3": {
    "pom": "sha256-oQvtmKrkapQj/eE719L60v+wIjz/WY/MjbzA72a7wyg="
   },
+  "com/github/javaparser#javaparser-parent/3.28.2": {
+   "pom": "sha256-A1jOdbyhpUwUHha38WIelz+hd932T+ArDzjfI61ABUM="
+  },
   "com/google/code/findbugs#jsr305/3.0.2": {
    "jar": "sha256-dmrSoHg/JoeWLIrXTO7MOKKLn3Ki0IXuQ4t4E+ko0Mc=",
    "pom": "sha256-GYidvfGyVLJgGl7mRbgUepdGRIgil2hMeYr+XWPXjf4="
@@ -349,6 +356,10 @@
    "jar": "sha256-cAQAep/Yf+HYb2c7RywDcuW8ULrLckwCmmES18S0pkA=",
    "pom": "sha256-CmVT5rRPYUi1qZu7q1MyudxDngdXpYniQZBgvfsC/Oo="
   },
+  "org/junit#junit-bom/5.14.4": {
+   "module": "sha256-il6Y0THefXqtse6Iv9htZuYqfC4qQHSjskmLA9I262Q=",
+   "pom": "sha256-Vwbo8poKB/Vu+76koGcHk0FBlLuNJNgUO6Hnh6LzKFY="
+  },
   "org/junit#junit-bom/5.7.1": {
    "module": "sha256-mFTjiU1kskhSB+AEa8oHs9QtFp54L0+oyc4imnj67gQ=",
    "pom": "sha256-C5sUo9YhBvr+jGinF7h7h60YaFiZRRt1PAT6QbaFd4Q="
diff --git a/pkgs/by-name/mi/mindustry/package.nix b/pkgs/by-name/mi/mindustry/package.nix
index 3c2465d98eed..14e781292309 100644
--- a/pkgs/by-name/mi/mindustry/package.nix
+++ b/pkgs/by-name/mi/mindustry/package.nix
@@ -38,7 +38,7 @@
 
 let
   pname = "mindustry";
-  version = "159.3";
+  version = "160.4";
   buildVersion = makeBuildVersion version;
 
   jdk = jdk17;
@@ -48,21 +48,21 @@ let
     owner = "Anuken";
     repo = "Mindustry";
     tag = "v${version}";
-    hash = "sha256-i29EbiKBVWab9YJWPWeVFQLLvRcigvHJPc7803A5e6g=";
+    hash = "sha256-gWAsYavRkRfdJ89IHrbK89Jwp/Whvu2FnswlJBb1rfQ=";
   };
   Arc = fetchFromGitHub {
     name = "Arc-source";
     owner = "Anuken";
     repo = "Arc";
     tag = "v${version}";
-    hash = "sha256-1HEPON+cfsPYhPtYwVhj7zrc7fMdwpOA6H2r8yp4erE=";
+    hash = "sha256-V4j0VNwcc1C5xaWiE1cPEKLah+ba3ahPANPEVi43cCE=";
   };
   soloud = fetchFromGitHub {
     owner = "Anuken";
     repo = "soloud";
     # This is pinned in Arc's build.gradle
-    tag = "2026.06.01";
-    hash = "sha256-0/A3myfCYb+AMP3WH6stmXeb1eiA4dgX6H1Quj4AD9Q=";
+    tag = "2026.09.04";
+    hash = "sha256-g8ZELw+hB9x7/HnmNzvXihGTBqpigdtScvYbrhvlZVM=";
   };
 
   desktopItem = makeDesktopItem {
@@ -118,6 +118,20 @@ stdenv.mkDerivation {
     touch build/jnigen/sources/sdlmingw.tar.gz
     popd
 
+    # force jnigen to use nixpkgs cc-wrapper
+    for file in \
+      Arc/arc-core/build.gradle \
+      Arc/extensions/freetype/build.gradle \
+      Arc/extensions/filedialogs/build.gradle
+    do
+      substituteInPlace "$file" \
+        --replace-fail "addLinux(x64, x86)" "addLinux(x64, x86)
+            each({it.os == Linux}){ compilerPrefix = '${stdenv.cc}/bin/' }"
+    done
+    substituteInPlace Arc/backends/backend-sdl/build.gradle \
+      --replace-fail "addLinux(x64, x86){" "addLinux(x64, x86){
+          compilerPrefix = '${stdenv.cc}/bin/'"
+
     cd Mindustry
 
     # Remove unbuildable iOS stuff
diff --git a/pkgs/by-name/mo/moosefs/package.nix b/pkgs/by-name/mo/moosefs/package.nix
index f7744c5edc44..710e0626ad00 100644
--- a/pkgs/by-name/mo/moosefs/package.nix
+++ b/pkgs/by-name/mo/moosefs/package.nix
@@ -58,6 +58,8 @@ stdenv.mkDerivation (finalAttrs: {
   };
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     homepage = "https://moosefs.com";
     description = "Open Source, Petabyte, Fault-Tolerant, Highly Performing, Scalable Network Distributed File System";
     platforms = lib.platforms.unix;
diff --git a/pkgs/by-name/mu/mucommander/package.nix b/pkgs/by-name/mu/mucommander/package.nix
index 80dd3c7eae5e..71995d53328d 100644
--- a/pkgs/by-name/mu/mucommander/package.nix
+++ b/pkgs/by-name/mu/mucommander/package.nix
@@ -53,6 +53,8 @@ stdenv.mkDerivation (finalAttrs: {
   '';
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     homepage = "https://www.mucommander.com/";
     description = "Cross-platform file manager";
     license = lib.licenses.gpl3;
diff --git a/pkgs/by-name/n8/n8n/package.nix b/pkgs/by-name/n8/n8n/package.nix
index 999fc64cc9b3..90aefea770fa 100644
--- a/pkgs/by-name/n8/n8n/package.nix
+++ b/pkgs/by-name/n8/n8n/package.nix
@@ -27,20 +27,20 @@ let
 in
 stdenv.mkDerivation (finalAttrs: {
   pname = "n8n";
-  version = "2.37.10";
+  version = "2.39.6";
 
   src = fetchFromGitHub {
     owner = "n8n-io";
     repo = "n8n";
     tag = "n8n@${finalAttrs.version}";
-    hash = "sha256-cEWwXiyBLiZ8MgH5OKe0+hgd9ooYZTDQIuS4Dq0nKos=";
+    hash = "sha256-fmo0xL6IF6J+D5ZamkoBXyZ4Q8s3l5MeBWaXc39OsTU=";
   };
 
   pnpmDeps = fetchPnpmDeps {
     inherit (finalAttrs) pname version src;
     pnpm = pnpm_11;
     fetcherVersion = 4;
-    hash = "sha256-T1axKjZT1I8NjXFV8hAKSYa+zCl/Fpyzz2DGM+cmkLQ=";
+    hash = "sha256-yL95w+Jd5I5R6r/qNihvAJ4MX2LMyS9ICZzJnLxHR4s=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/by-name/no/nomnatong/package.nix b/pkgs/by-name/no/nomnatong/package.nix
index 5194edbde436..9372d1d15699 100644
--- a/pkgs/by-name/no/nomnatong/package.nix
+++ b/pkgs/by-name/no/nomnatong/package.nix
@@ -9,13 +9,13 @@
 
 stdenvNoCC.mkDerivation (finalAttrs: {
   pname = "nomnatong";
-  version = "5.17";
+  version = "5.18";
 
   src = fetchFromGitHub {
     owner = "nomfoundation";
     repo = "font";
     rev = "v${finalAttrs.version}";
-    hash = "sha256-Z/Q0WLr+kSDIiAwqrZUokoiWUp5qP25rXgqlPlMo0hg=";
+    hash = "sha256-4kBEWYm7OvJbPFqum0zYTclsVpK4BECHtYoaH84ZyGo=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/by-name/ob/obscura/package.nix b/pkgs/by-name/ob/obscura/package.nix
index 05039b81a67a..2b0e776f0b3f 100644
--- a/pkgs/by-name/ob/obscura/package.nix
+++ b/pkgs/by-name/ob/obscura/package.nix
@@ -16,16 +16,16 @@ in
 rustPlatform.buildRustPackage rec {
   pname = "obscura";
   __structuredAttrs = true;
-  version = "0.2.0";
+  version = "0.2.2";
 
   src = fetchFromGitHub {
     owner = "h4ckf0r0day";
     repo = "obscura";
     rev = "v${version}";
-    hash = "sha256-f09I77mKhQA1mCt8YmtVqbK/QIb9MrvhpYav+FJdkRI=";
+    hash = "sha256-ponNfeiRO4ajUYRZ3Pz3JYtPW1j8OP5jGDSF/a6PYuw=";
   };
 
-  cargoHash = "sha256-tBuPQjjqXkF+vcBRXXyi9+gcBzg8L3QH2jjixBzGODE=";
+  cargoHash = "sha256-YUKy5m6gOHD62kcOuk/o3oj1MfudeetBQV4q5asaOqQ=";
 
   nativeBuildInputs = [
     pkg-config
@@ -51,7 +51,7 @@ rustPlatform.buildRustPackage rec {
     OPENSSL_NO_VENDOR = 1;
     RUSTY_V8_ARCHIVE = librusty_v8;
     # Upstream never bumps the workspace Cargo.toml version per release (still
-    # 0.1.0 at the v0.2.0 tag); obscura-cli/build.rs only reports the git tag
+    # 0.1.0 at the v0.2.2 tag); obscura-cli/build.rs only reports the git tag
     # on GitHub Actions and otherwise falls back to CARGO_PKG_VERSION. Pin it
     # here so `obscura --version` matches the packaged release.
     OBSCURA_VERSION = version;
diff --git a/pkgs/by-name/ol/olympus-unwrapped/package.nix b/pkgs/by-name/ol/olympus-unwrapped/package.nix
index 3030ff0ad8de..f28947dc0e8c 100644
--- a/pkgs/by-name/ol/olympus-unwrapped/package.nix
+++ b/pkgs/by-name/ol/olympus-unwrapped/package.nix
@@ -22,9 +22,9 @@ let
 
   phome = "$out/lib/olympus";
   # The following variables are to be updated by the update script.
-  version = "26.09.06.01";
-  buildId = "5847"; # IMPORTANT: This line is matched with regex in update.sh.
-  rev = "578d4c963a132f5d8c33933655acab9a74a12429";
+  version = "26.09.15.05";
+  buildId = "5878"; # IMPORTANT: This line is matched with regex in update.sh.
+  rev = "2472132ac23a30701c1eb928dbd95858113ded25";
 in
 buildDotnetModule {
   pname = "olympus-unwrapped";
@@ -37,7 +37,7 @@ buildDotnetModule {
     owner = "EverestAPI";
     repo = "Olympus";
     fetchSubmodules = true; # Required. See upstream's README.
-    hash = "sha256-1nij3wldq6q6BBV/CSvgVqe7OLvvu+QSIhFQdIVVa6c=";
+    hash = "sha256-pQjRiVVpF2J7qR6BfvdC/jkHGVcUJsXmq1tUTs7GmmY=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/by-name/om/omp/package.nix b/pkgs/by-name/om/omp/package.nix
index a8bce2a29dd6..bbeb744c9ee9 100644
--- a/pkgs/by-name/om/omp/package.nix
+++ b/pkgs/by-name/om/omp/package.nix
@@ -32,7 +32,7 @@ let
 in
 stdenv.mkDerivation (finalAttrs: {
   pname = "omp";
-  version = "18.2.1";
+  version = "18.2.4";
 
   strictDeps = true;
   __structuredAttrs = true;
@@ -41,12 +41,12 @@ stdenv.mkDerivation (finalAttrs: {
     owner = "can1357";
     repo = "oh-my-pi";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-Xxce8dTViESlYF0koYujNHH7lbZj+BRA9tvgOKXmQ7s=";
+    hash = "sha256-z07Nx7SUtdqcIc+Py5xwr6xZz4sDwply69dbhyTJ1L4=";
   };
 
   cargoDeps = rustPlatform.fetchCargoVendor {
     inherit (finalAttrs) src;
-    hash = "sha256-PIsVh8HAIuUIoi8K8vExBKurGM86RSebB4f475jdai8=";
+    hash = "sha256-x4zJnk1rdByqRx1jFcOuKwyqbbxaQ9K6zHDBxOIa+7Y=";
   };
 
   postPatch = ''
@@ -91,7 +91,7 @@ stdenv.mkDerivation (finalAttrs: {
     # Prevents breaking symlinks in node_modules
     dontFixup = true;
 
-    outputHash = "sha256-EeOZ7XTDjSHH6QtcqOVBQQeXMh47GhCOPXHTB52VeOA=";
+    outputHash = "sha256-NNxfvvLKpAjlrHS/nzGVSDQ+ZHC4ayjJa7fcIapleZw=";
     outputHashMode = "recursive";
   };
 
diff --git a/pkgs/by-name/os/osrm-backend/package.nix b/pkgs/by-name/os/osrm-backend/package.nix
index 9e7282fe669c..d7ec50185862 100644
--- a/pkgs/by-name/os/osrm-backend/package.nix
+++ b/pkgs/by-name/os/osrm-backend/package.nix
@@ -59,6 +59,8 @@ stdenv.mkDerivation (finalAttrs: {
   };
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     homepage = "https://project-osrm.org/";
     description = "Open Source Routing Machine computes shortest paths in a graph. It was designed to run well with map data from the Openstreetmap Project";
     changelog = "https://github.com/Project-OSRM/osrm-backend/releases/tag/${finalAttrs.src.tag}";
diff --git a/pkgs/by-name/pr/prometheus-mikrotik-exporter/package.nix b/pkgs/by-name/pr/prometheus-mikrotik-exporter/package.nix
index bb6186dcbeab..b12ee91cf660 100644
--- a/pkgs/by-name/pr/prometheus-mikrotik-exporter/package.nix
+++ b/pkgs/by-name/pr/prometheus-mikrotik-exporter/package.nix
@@ -3,6 +3,7 @@
   buildGoModule,
   fetchFromGitHub,
   nixosTests,
+  stdenv, # for meta.broken
 }:
 
 buildGoModule rec {
@@ -23,6 +24,8 @@ buildGoModule rec {
   passthru.tests = { inherit (nixosTests.prometheus-exporters) mikrotik; };
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     inherit (src.meta) homepage;
     description = "Prometheus MikroTik device(s) exporter";
     mainProgram = "mikrotik-exporter";
diff --git a/pkgs/by-name/pr/protoc-gen-js/package.nix b/pkgs/by-name/pr/protoc-gen-js/package.nix
index 5d16360767f7..b61a7a74cc8e 100644
--- a/pkgs/by-name/pr/protoc-gen-js/package.nix
+++ b/pkgs/by-name/pr/protoc-gen-js/package.nix
@@ -58,6 +58,8 @@ buildBazelPackage' rec {
   '';
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "Protobuf plugin for generating JavaScript code";
     mainProgram = "protoc-gen-js";
     homepage = "https://github.com/protocolbuffers/protobuf-javascript";
diff --git a/pkgs/by-name/py/pyright/package-lock.json b/pkgs/by-name/py/pyright/package-lock.json
deleted file mode 100644
index b2ba1a8c0b9e..000000000000
--- a/pkgs/by-name/py/pyright/package-lock.json
+++ /dev/null
@@ -1,256 +0,0 @@
-{
-  "name": "pyright-root",
-  "lockfileVersion": 3,
-  "requires": true,
-  "packages": {
-    "": {
-      "name": "pyright-root",
-      "devDependencies": {
-        "glob": "^11.1.0",
-        "jsonc-parser": "^3.3.1"
-      }
-    },
-    "node_modules/@isaacs/cliui": {
-      "version": "9.0.0",
-      "resolved": "https://registry.npmjs.org/@isaacs/cliui/-/cliui-9.0.0.tgz",
-      "integrity": "sha512-AokJm4tuBHillT+FpMtxQ60n8ObyXBatq7jD2/JA9dxbDDokKQm8KMht5ibGzLVU9IJDIKK4TPKgMHEYMn3lMg==",
-      "dev": true,
-      "license": "BlueOak-1.0.0",
-      "engines": {
-        "node": ">=18"
-      }
-    },
-    "node_modules/balanced-match": {
-      "version": "4.0.4",
-      "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-4.0.4.tgz",
-      "integrity": "sha512-BLrgEcRTwX2o6gGxGOCNyMvGSp35YofuYzw9h1IMTRmKqttAZZVU67bdb9Pr2vUHA8+j3i2tJfjO6C6+4myGTA==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": "18 || 20 || >=22"
-      }
-    },
-    "node_modules/brace-expansion": {
-      "version": "5.0.9",
-      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-5.0.9.tgz",
-      "integrity": "sha512-ScQ4IuvIEF1TMlP7Zt+vjJ//9zlPb2SDcxWxM3bk8s6t6GGdJ7KO1dCcTidOPJKePW30LE/2cT7wCyPho9/Wxg==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "balanced-match": "^4.0.2"
-      },
-      "engines": {
-        "node": "20 || >=22"
-      }
-    },
-    "node_modules/cross-spawn": {
-      "version": "7.0.6",
-      "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.6.tgz",
-      "integrity": "sha512-uV2QOWP2nWzsy2aMp8aRibhi9dlzF5Hgh5SHaB9OiTGEyDTiJJyx0uy51QXdyWbtAHNua4XJzUKca3OzKUd3vA==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "path-key": "^3.1.0",
-        "shebang-command": "^2.0.0",
-        "which": "^2.0.1"
-      },
-      "engines": {
-        "node": ">= 8"
-      }
-    },
-    "node_modules/foreground-child": {
-      "version": "3.3.1",
-      "resolved": "https://registry.npmjs.org/foreground-child/-/foreground-child-3.3.1.tgz",
-      "integrity": "sha512-gIXjKqtFuWEgzFRJA9WCQeSJLZDjgJUOMCMzxtvFq/37KojM1BFGufqsCy0r4qSQmYLsZYMeyRqzIWOMup03sw==",
-      "dev": true,
-      "license": "ISC",
-      "dependencies": {
-        "cross-spawn": "^7.0.6",
-        "signal-exit": "^4.0.1"
-      },
-      "engines": {
-        "node": ">=14"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/isaacs"
-      }
-    },
-    "node_modules/glob": {
-      "version": "11.1.0",
-      "resolved": "https://registry.npmjs.org/glob/-/glob-11.1.0.tgz",
-      "integrity": "sha512-vuNwKSaKiqm7g0THUBu2x7ckSs3XJLXE+2ssL7/MfTGPLLcrJQ/4Uq1CjPTtO5cCIiRxqvN6Twy1qOwhL0Xjcw==",
-      "deprecated": "Old versions of glob are not supported, and contain widely publicized security vulnerabilities, which have been fixed in the current version. Please update. Support for old versions may be purchased (at exorbitant rates) by contacting i@izs.me",
-      "dev": true,
-      "license": "BlueOak-1.0.0",
-      "dependencies": {
-        "foreground-child": "^3.3.1",
-        "jackspeak": "^4.1.1",
-        "minimatch": "^10.1.1",
-        "minipass": "^7.1.2",
-        "package-json-from-dist": "^1.0.0",
-        "path-scurry": "^2.0.0"
-      },
-      "bin": {
-        "glob": "dist/esm/bin.mjs"
-      },
-      "engines": {
-        "node": "20 || >=22"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/isaacs"
-      }
-    },
-    "node_modules/isexe": {
-      "version": "2.0.0",
-      "resolved": "https://registry.npmjs.org/isexe/-/isexe-2.0.0.tgz",
-      "integrity": "sha512-RHxMLp9lnKHGHRng9QFhRCMbYAcVpn69smSGcq3f36xjgVVWThj4qqLbTLlq7Ssj8B+fIQ1EuCEGI2lKsyQeIw==",
-      "dev": true,
-      "license": "ISC"
-    },
-    "node_modules/jackspeak": {
-      "version": "4.2.3",
-      "resolved": "https://registry.npmjs.org/jackspeak/-/jackspeak-4.2.3.tgz",
-      "integrity": "sha512-ykkVRwrYvFm1nb2AJfKKYPr0emF6IiXDYUaFx4Zn9ZuIH7MrzEZ3sD5RlqGXNRpHtvUHJyOnCEFxOlNDtGo7wg==",
-      "dev": true,
-      "license": "BlueOak-1.0.0",
-      "dependencies": {
-        "@isaacs/cliui": "^9.0.0"
-      },
-      "engines": {
-        "node": "20 || >=22"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/isaacs"
-      }
-    },
-    "node_modules/jsonc-parser": {
-      "version": "3.3.1",
-      "resolved": "https://registry.npmjs.org/jsonc-parser/-/jsonc-parser-3.3.1.tgz",
-      "integrity": "sha512-HUgH65KyejrUFPvHFPbqOY0rsFip3Bo5wb4ngvdi1EpCYWUQDC5V+Y7mZws+DLkr4M//zQJoanu1SP+87Dv1oQ==",
-      "dev": true,
-      "license": "MIT"
-    },
-    "node_modules/lru-cache": {
-      "version": "11.5.2",
-      "resolved": "https://registry.npmjs.org/lru-cache/-/lru-cache-11.5.2.tgz",
-      "integrity": "sha512-4pfM1Ff0x50o0tQwb5ucw/RzNyD0/YJME6IVcStalZuMWxdt3sR3huStTtxz4PUmvZfRguvDejasvQ2kifR11g==",
-      "dev": true,
-      "license": "BlueOak-1.0.0",
-      "engines": {
-        "node": "20 || >=22"
-      }
-    },
-    "node_modules/minimatch": {
-      "version": "10.2.6",
-      "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-10.2.6.tgz",
-      "integrity": "sha512-vpLQEs+VLCr1nU0BXS07maYoFwlDAH0gngQuuttxIwutDFEMHq2blX+8vpgxDdK3J1PwjCJiep77OitTZ4Ll1A==",
-      "dev": true,
-      "license": "BlueOak-1.0.0",
-      "dependencies": {
-        "brace-expansion": "^5.0.8"
-      },
-      "engines": {
-        "node": "18 || 20 || >=22"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/isaacs"
-      }
-    },
-    "node_modules/minipass": {
-      "version": "7.1.3",
-      "resolved": "https://registry.npmjs.org/minipass/-/minipass-7.1.3.tgz",
-      "integrity": "sha512-tEBHqDnIoM/1rXME1zgka9g6Q2lcoCkxHLuc7ODJ5BxbP5d4c2Z5cGgtXAku59200Cx7diuHTOYfSBD8n6mm8A==",
-      "dev": true,
-      "license": "BlueOak-1.0.0",
-      "engines": {
-        "node": ">=16 || 14 >=14.17"
-      }
-    },
-    "node_modules/package-json-from-dist": {
-      "version": "1.0.1",
-      "resolved": "https://registry.npmjs.org/package-json-from-dist/-/package-json-from-dist-1.0.1.tgz",
-      "integrity": "sha512-UEZIS3/by4OC8vL3P2dTXRETpebLI2NiI5vIrjaD/5UtrkFX/tNbwjTSRAGC/+7CAo2pIcBaRgWmcBBHcsaCIw==",
-      "dev": true,
-      "license": "BlueOak-1.0.0"
-    },
-    "node_modules/path-key": {
-      "version": "3.1.1",
-      "resolved": "https://registry.npmjs.org/path-key/-/path-key-3.1.1.tgz",
-      "integrity": "sha512-ojmeN0qd+y0jszEtoY48r0Peq5dwMEkIlCOu6Q5f41lfkswXuKtYrhgoTpLnyIcHm24Uhqx+5Tqm2InSwLhE6Q==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=8"
-      }
-    },
-    "node_modules/path-scurry": {
-      "version": "2.0.2",
-      "resolved": "https://registry.npmjs.org/path-scurry/-/path-scurry-2.0.2.tgz",
-      "integrity": "sha512-3O/iVVsJAPsOnpwWIeD+d6z/7PmqApyQePUtCndjatj/9I5LylHvt5qluFaBT3I5h3r1ejfR056c+FCv+NnNXg==",
-      "dev": true,
-      "license": "BlueOak-1.0.0",
-      "dependencies": {
-        "lru-cache": "^11.0.0",
-        "minipass": "^7.1.2"
-      },
-      "engines": {
-        "node": "18 || 20 || >=22"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/isaacs"
-      }
-    },
-    "node_modules/shebang-command": {
-      "version": "2.0.0",
-      "resolved": "https://registry.npmjs.org/shebang-command/-/shebang-command-2.0.0.tgz",
-      "integrity": "sha512-kHxr2zZpYtdmrN1qDjrrX/Z1rR1kG8Dx+gkpK1G4eXmvXswmcE1hTWBWYUzlraYw1/yZp6YuDY77YtvbN0dmDA==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "shebang-regex": "^3.0.0"
-      },
-      "engines": {
-        "node": ">=8"
-      }
-    },
-    "node_modules/shebang-regex": {
-      "version": "3.0.0",
-      "resolved": "https://registry.npmjs.org/shebang-regex/-/shebang-regex-3.0.0.tgz",
-      "integrity": "sha512-7++dFhtcx3353uBaq8DDR4NuxBetBzC7ZQOhmTQInHEd6bSrXdiEyzCvG07Z44UYdLShWUyXt5M/yhz8ekcb1A==",
-      "dev": true,
-      "license": "MIT",
-      "engines": {
-        "node": ">=8"
-      }
-    },
-    "node_modules/signal-exit": {
-      "version": "4.1.0",
-      "resolved": "https://registry.npmjs.org/signal-exit/-/signal-exit-4.1.0.tgz",
-      "integrity": "sha512-bzyZ1e88w9O1iNJbKnOlvYTrWPDl46O1bG0D3XInv+9tkPrxrN8jUUTiFlDkkmKWgn1M6CfIA13SuGqOa9Korw==",
-      "dev": true,
-      "license": "ISC",
-      "engines": {
-        "node": ">=14"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/isaacs"
-      }
-    },
-    "node_modules/which": {
-      "version": "2.0.2",
-      "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz",
-      "integrity": "sha512-BLI3Tl1TW3Pvl70l3yq3Y64i+awpwXqsGBYWkkqMtnbXgrMD+yj7rhW0kuEDxzJaYXGjEW5ogapKNMEKNMjibA==",
-      "dev": true,
-      "license": "ISC",
-      "dependencies": {
-        "isexe": "^2.0.0"
-      },
-      "bin": {
-        "node-which": "bin/node-which"
-      },
-      "engines": {
-        "node": ">= 8"
-      }
-    }
-  }
-}
diff --git a/pkgs/by-name/py/pyright/package.nix b/pkgs/by-name/py/pyright/package.nix
index 05523336b9bb..e21dc5a183b1 100644
--- a/pkgs/by-name/py/pyright/package.nix
+++ b/pkgs/by-name/py/pyright/package.nix
@@ -1,87 +1,90 @@
 {
   lib,
-  buildNpmPackage,
+  stdenv,
   fetchFromGitHub,
-  runCommand,
-  jq,
+  fetchPnpmDeps,
+  pnpm_11,
+  pnpmConfigHook,
+  nodejs,
+  makeBinaryWrapper,
+  nix-update-script,
+  testers,
 }:
 
-let
-  version = "1.1.412";
+stdenv.mkDerivation (finalAttrs: {
+  pname = "pyright";
+  version = "1.1.414";
+
+  __structuredAttrs = true;
+  strictDeps = true;
 
   src = fetchFromGitHub {
     owner = "Microsoft";
     repo = "pyright";
-    tag = version;
-    hash = "sha256-V2sQp/LA43NjCdtr2/drZ1LMgm4u2tcf4EjdhWVLXHw=";
+    tag = finalAttrs.version;
+    hash = "sha256-rNlRQSkKgIGcHje1YonWsX5oXAAmFxfwq3aA1R5p7HA=";
   };
 
-  patchedPackageJSON =
-    runCommand "package.json"
-      {
-        nativeBuildInputs = [ jq ];
-      }
-      ''
-        jq '
-          .devDependencies |= with_entries(select(.key == "glob" or .key == "jsonc-parser"))
-          | .scripts =  {  }
-          ' ${src}/package.json > $out
-      '';
+  pnpmWorkspaces = [
+    "pyright-root"
+    "pyright-internal"
+    "pyright"
+  ];
 
-  pyright-root = buildNpmPackage {
-    pname = "pyright-root";
-    inherit version src;
-    sourceRoot = "${src.name}"; # required for update.sh script
-    npmDepsHash = "sha256-0w/CYFfAaEK6LKZZc9+nt5zUmxCqCcJfSZRAroOhJOA=";
-    dontNpmBuild = true;
-    postPatch = ''
-      cp ${patchedPackageJSON} ./package.json
-      cp ${./package-lock.json} ./package-lock.json
-    '';
-    installPhase = ''
-      runHook preInstall
-      cp -r . "$out"
-      runHook postInstall
-    '';
+  pnpmDeps = fetchPnpmDeps {
+    inherit (finalAttrs)
+      pname
+      version
+      src
+      pnpmWorkspaces
+      ;
+    pnpm = pnpm_11;
+    fetcherVersion = 4;
+    hash = "sha256-FZl5XSiA0uEH3lZxOxzLpD0ZY8vmZuxLIxAxh7kqPKo=";
   };
 
-  pyright-internal = buildNpmPackage {
-    pname = "pyright-internal";
-    inherit version src;
-    sourceRoot = "${src.name}/packages/pyright-internal";
-    npmDepsHash = "sha256-skTnHcET5ujyKTEqh3oyiBwHF6yvaY8c/ccOnwQQKJ0=";
-    dontNpmBuild = true;
-    installPhase = ''
-      runHook preInstall
-      cp -r . "$out"
-      runHook postInstall
-    '';
-  };
-in
-buildNpmPackage rec {
-  pname = "pyright";
-  inherit version src;
+  nativeBuildInputs = [
+    nodejs
+    pnpm_11
+    pnpmConfigHook
+    makeBinaryWrapper
+  ];
 
-  sourceRoot = "${src.name}/packages/pyright";
-  npmDepsHash = "sha256-rgENiJVYKMSZimWzlvaaiC6Z5/OEdk4W47gkjcuv0nw=";
+  buildPhase = ''
+    runHook preBuild
 
-  postPatch = ''
-    chmod +w ../../
-    ln -s ${pyright-root}/node_modules ../../node_modules
-    chmod +w ../pyright-internal
-    ln -s ${pyright-internal}/node_modules ../pyright-internal/node_modules
+    pnpm --filter pyright build
+
+    runHook postBuild
   '';
 
-  dontNpmBuild = true;
+  installPhase = ''
+    runHook preInstall
 
-  passthru.updateScript = ./update.sh;
+    mkdir -p "$out/lib/pyright"
+    cp -r packages/pyright/{dist,index.js,langserver.index.js,package.json} "$out/lib/pyright/"
+    cp LICENSE.txt README.md "$out/lib/pyright/"
+
+    makeWrapper ${lib.getExe nodejs} "$out/bin/pyright" \
+      --add-flags "$out/lib/pyright/index.js"
+    makeWrapper ${lib.getExe nodejs} "$out/bin/pyright-langserver" \
+      --add-flags "$out/lib/pyright/langserver.index.js"
+
+    runHook postInstall
+  '';
+
+  passthru = {
+    updateScript = nix-update-script { };
+    tests.version = testers.testVersion { package = finalAttrs.finalPackage; };
+  };
 
   meta = {
-    changelog = "https://github.com/Microsoft/pyright/releases/tag/${src.tag}";
+    changelog = "https://github.com/Microsoft/pyright/releases/tag/${finalAttrs.src.tag}";
     description = "Type checker for the Python language";
     homepage = "https://github.com/Microsoft/pyright";
     license = lib.licenses.mit;
     mainProgram = "pyright";
     maintainers = with lib.maintainers; [ kalekseev ];
+    platforms = nodejs.meta.platforms;
   };
-}
+})
diff --git a/pkgs/by-name/py/pyright/update.sh b/pkgs/by-name/py/pyright/update.sh
deleted file mode 100755
index a52bdec5480f..000000000000
--- a/pkgs/by-name/py/pyright/update.sh
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/usr/bin/env nix-shell
-#!nix-shell -i bash -p curl gnused common-updater-scripts jq prefetch-npm-deps nodejs
-set -euo pipefail
-
-version=$(curl ${GITHUB_TOKEN:+" -u \":$GITHUB_TOKEN\""} -s https://api.github.com/repos/microsoft/pyright/releases/latest | jq -r '.tag_name | sub("^v"; "")')
-
-update-source-version pyright "$version"
-
-root="$(dirname "$(readlink -f "$0")")"
-FILE_PATH="$root/package.nix"
-REPO_URL_PREFIX="https://github.com/microsoft/pyright/raw"
-TEMP_DIR=$(mktemp -d)
-
-trap 'rm -rf "$TEMP_DIR"' EXIT
-
-# Function to download `package-lock.json` for a given source path and update hash
-update_hash() {
-    local source_root_path="$1"
-    local existing_hash="$2"
-
-    local package_url="${REPO_URL_PREFIX}/${version}${source_root_path}"
-    if [ "$source_root_path" == "" ]; then
-        pushd "${TEMP_DIR}"
-        curl -fsSL "$package_url/package.json" | jq '
-          .devDependencies |= with_entries(select(.key == "glob" or .key == "jsonc-parser"))
-          | .scripts =  {  }
-        ' > package.json
-        npm install --package-lock
-        cp package-lock.json "$root/package-lock.json"
-        popd
-    else
-        curl -fsSL -o "${TEMP_DIR}/package-lock.json" "$package_url/package-lock.json"
-    fi
-
-    # Calculate the new hash
-    local new_hash
-    new_hash=$(prefetch-npm-deps "${TEMP_DIR}/package-lock.json")
-
-    # Update npmDepsHash in the original file
-    sed -i "s|$existing_hash|${new_hash}|" "$FILE_PATH"
-}
-
-while IFS= read -r source_root_line; do
-    [[ "$source_root_line" =~ sourceRoot ]] || continue
-    source_root_path=$(echo "$source_root_line" | sed -e 's/^.*"${src.name}\(.*\)";.*$/\1/')
-
-    # Extract the current npmDepsHash for this sourceRoot
-    existing_hash=$(grep -A1 "$source_root_line" "$FILE_PATH" | grep 'npmDepsHash' | sed -e 's/^.*npmDepsHash = "\(.*\)";$/\1/')
-
-    # Call the function to download and update the hash
-    update_hash "$source_root_path" "$existing_hash"
-done < "$FILE_PATH"
diff --git a/pkgs/by-name/qu/quaternion/package.nix b/pkgs/by-name/qu/quaternion/package.nix
index 209c96528916..ecdfc67023a2 100644
--- a/pkgs/by-name/qu/quaternion/package.nix
+++ b/pkgs/by-name/qu/quaternion/package.nix
@@ -51,6 +51,8 @@ stdenv.mkDerivation (finalAttrs: {
       '';
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "Cross-platform desktop IM client for the Matrix protocol";
     mainProgram = "quaternion";
     homepage = "https://matrix.org/ecosystem/clients/quaternion/";
diff --git a/pkgs/by-name/re/recoll/package.nix b/pkgs/by-name/re/recoll/package.nix
index f90707fa4b4d..cdffbfe18ee5 100644
--- a/pkgs/by-name/re/recoll/package.nix
+++ b/pkgs/by-name/re/recoll/package.nix
@@ -209,8 +209,10 @@ stdenv.mkDerivation rec {
     maintainers = with lib.maintainers; [
       jcumming
     ];
-
+    # last successful hydra build on darwin was in 2024
     # `Makefile.am` assumes the ability to run the hostPlatform's python binary at build time
-    broken = withPython && (with stdenv; !buildPlatform.canExecute hostPlatform);
+    broken =
+      stdenv.hostPlatform.isDarwin
+      || (withPython && !stdenv.buildPlatform.canExecute stdenv.hostPlatform);
   };
 }
diff --git a/pkgs/by-name/ro/rosie/package.nix b/pkgs/by-name/ro/rosie/package.nix
index 0c59aa6f755d..987c9c44baf4 100644
--- a/pkgs/by-name/ro/rosie/package.nix
+++ b/pkgs/by-name/ro/rosie/package.nix
@@ -56,6 +56,8 @@ stdenv.mkDerivation (finalAttrs: {
   ];
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     homepage = "https://rosie-lang.org";
     description = "Tools for searching using parsing expression grammars";
     mainProgram = "rosie";
diff --git a/pkgs/by-name/rv/rvvm/package.nix b/pkgs/by-name/rv/rvvm/package.nix
index bcc11a05f076..4f953720e1fd 100644
--- a/pkgs/by-name/rv/rvvm/package.nix
+++ b/pkgs/by-name/rv/rvvm/package.nix
@@ -57,6 +57,8 @@ stdenv.mkDerivation (finalAttrs: {
   ++ lib.optional (!enableSDL && !enableX11) "USE_FB=0";
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     homepage = "https://github.com/LekKit/RVVM";
     description = "RISC-V Virtual Machine";
     license = with lib.licenses; [
diff --git a/pkgs/by-name/sg/sgfutils/package.nix b/pkgs/by-name/sg/sgfutils/package.nix
index 138de47b1987..12a1a25d0ad0 100644
--- a/pkgs/by-name/sg/sgfutils/package.nix
+++ b/pkgs/by-name/sg/sgfutils/package.nix
@@ -43,6 +43,8 @@ stdenv.mkDerivation {
       --set-default FONTCONFIG_FILE ${makeFontsConf { fontDirectories = [ ]; }}
   '';
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     homepage = "https://homepages.cwi.nl/~aeb/go/sgfutils/html/sgfutils.html";
     description = "Command line utilities that help working with SGF files";
     longDescription = ''
diff --git a/pkgs/by-name/si/simple-mtpfs/package.nix b/pkgs/by-name/si/simple-mtpfs/package.nix
deleted file mode 100644
index 6cbb753e16f1..000000000000
--- a/pkgs/by-name/si/simple-mtpfs/package.nix
+++ /dev/null
@@ -1,40 +0,0 @@
-{
-  stdenv,
-  lib,
-  fetchFromGitHub,
-  autoreconfHook,
-  autoconf-archive,
-  pkg-config,
-  fuse,
-  libmtp,
-}:
-stdenv.mkDerivation (finalAttrs: {
-  pname = "simple-mtpfs";
-  version = "0.4.0";
-
-  src = fetchFromGitHub {
-    owner = "phatina";
-    repo = "simple-mtpfs";
-    rev = "v${finalAttrs.version}";
-    hash = "sha256-vAqi2owa4LJK7y7S7TwkPAqDxzyHrZZBTu0MBwMT0gI=";
-  };
-
-  nativeBuildInputs = [
-    autoreconfHook
-    autoconf-archive
-    pkg-config
-  ];
-  buildInputs = [
-    fuse
-    libmtp
-  ];
-
-  meta = {
-    description = "Simple MTP fuse filesystem driver";
-    homepage = "https://github.com/phatina/simple-mtpfs";
-    license = lib.licenses.gpl2Plus;
-    platforms = lib.platforms.linux;
-    maintainers = with lib.maintainers; [ laalsaas ];
-    mainProgram = "simple-mtpfs";
-  };
-})
diff --git a/pkgs/by-name/ta/tabiew/package.nix b/pkgs/by-name/ta/tabiew/package.nix
index 67e0bffe6efd..3fb7fb7a1458 100644
--- a/pkgs/by-name/ta/tabiew/package.nix
+++ b/pkgs/by-name/ta/tabiew/package.nix
@@ -7,16 +7,16 @@
 }:
 rustPlatform.buildRustPackage (finalAttrs: {
   pname = "tabiew";
-  version = "0.15.0";
+  version = "0.15.1";
 
   src = fetchFromGitHub {
     owner = "shshemi";
     repo = "tabiew";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-iHdHeWx8xxqirwiGdeSbvHDXYPn1UkqoQMosaiakQz0=";
+    hash = "sha256-nsyCcdtGkPqmZBu7H7xRA60gB6aYCEr73/Lhx582fUY=";
   };
 
-  cargoHash = "sha256-MemnQS6lRmIzo9x94yorGIp2upTY/CW/3jGh73AdowQ=";
+  cargoHash = "sha256-Hi36D/cmTLr2c4rMwggz/5bGhc7nI1I+YJPAj8XSOXE=";
 
   nativeBuildInputs = [
     installShellFiles
diff --git a/pkgs/by-name/te/teos-watchtower-plugin/package.nix b/pkgs/by-name/te/teos-watchtower-plugin/package.nix
index 3da03f5357b4..5bfc810f7b16 100644
--- a/pkgs/by-name/te/teos-watchtower-plugin/package.nix
+++ b/pkgs/by-name/te/teos-watchtower-plugin/package.nix
@@ -6,6 +6,7 @@
   protobuf,
   rustfmt,
   openssl,
+  stdenv, # for meta.broken
 }:
 
 rustPlatform.buildRustPackage {
@@ -29,6 +30,8 @@ rustPlatform.buildRustPackage {
   __darwinAllowLocalNetworking = true;
 
   meta = teos.meta // {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "Lightning watchtower plugin for clightning";
     mainProgram = "watchtower-client";
   };
diff --git a/pkgs/by-name/ti/timekpr/package.nix b/pkgs/by-name/ti/timekpr/package.nix
index 5248b0546b4f..9cb5bfdc183a 100644
--- a/pkgs/by-name/ti/timekpr/package.nix
+++ b/pkgs/by-name/ti/timekpr/package.nix
@@ -13,12 +13,12 @@
 }:
 python3Packages.buildPythonApplication rec {
   pname = "timekpr";
-  version = "0.5.8";
+  version = "0.5.10";
 
   src = fetchgit {
     url = "https://git.launchpad.net/timekpr-next";
     tag = "v${version}";
-    hash = "sha256-Y0jAKl553HjoP59wJnKBKq4Ogko1cs8uazW2dy7AlBo=";
+    hash = "sha256-0vIMWIGVuyqU/eV9NmUvbBRwmONHgcmoqzPUI0XfCa0=";
   };
 
   buildInputs = [
@@ -71,6 +71,10 @@ python3Packages.buildPythonApplication rec {
       substituteInPlace bin/* **/*.py resource/server/systemd/timekpr.service \
         --replace-quiet /usr/lib/python3/dist-packages "$out"/${lib.escapeShellArg python3Packages.python.sitePackages}
 
+      # bin/* are /bin/sh launchers that exec /usr/bin/python3 in their body, which patchShebangs does not rewrite.
+      substituteInPlace bin/* \
+        --replace-fail /usr/bin/python3 ${lib.escapeShellArg python3Packages.python.interpreter}
+
       substituteInPlace **/*.desktop **/*.policy **/*.service \
         --replace-fail /usr/bin/timekpr "$out"/bin/timekpr
 
diff --git a/pkgs/by-name/to/torrserver/package.nix b/pkgs/by-name/to/torrserver/package.nix
index c6506ea52da4..60216e77f590 100644
--- a/pkgs/by-name/to/torrserver/package.nix
+++ b/pkgs/by-name/to/torrserver/package.nix
@@ -7,15 +7,15 @@
 }:
 buildGo126Module rec {
   pname = "torrserver";
-  version = "144.1";
+  version = "144.4";
 
   src = fetchFromGitHub {
     owner = "YouROK";
     repo = "TorrServer";
     tag = "MatriX.${version}";
-    sha256 = "sha256-55UMbOOvSI2o4jiEijx9Bs+pCjRnHSNobbFAAdEwcuo=";
+    sha256 = "sha256-R4aZE5eSslBS3kWSwo0W6rIdubmrJ2CCeElz1jYAt34=";
   };
-  vendorHash = "sha256-aO4/p+k1Pur73k4iwb8ULVrHy8mkPZbWYTuJf1Z7xTc=";
+  vendorHash = "sha256-/xlC2+aj07dNMz187z3bje+uHoIm7QuCPNwBUDQKBhI=";
 
   modRoot = "server";
   subPackages = [ "cmd" ];
diff --git a/pkgs/by-name/tr/transmission-rss/package.nix b/pkgs/by-name/tr/transmission-rss/package.nix
index a547bb976535..77eb892a2c52 100644
--- a/pkgs/by-name/tr/transmission-rss/package.nix
+++ b/pkgs/by-name/tr/transmission-rss/package.nix
@@ -4,6 +4,7 @@
   fetchFromGitHub,
   pkg-config,
   openssl,
+  stdenv, # for meta.broken
 }:
 
 rustPlatform.buildRustPackage {
@@ -27,6 +28,8 @@ rustPlatform.buildRustPackage {
   env.OPENSSL_NO_VENDOR = 1;
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "Add torrents to transmission based on RSS list";
     homepage = "https://github.com/herlon214/transmission-rss";
     maintainers = with lib.maintainers; [ icewind1991 ];
diff --git a/pkgs/by-name/un/uni/package.nix b/pkgs/by-name/un/uni/package.nix
index 3d1cfd790047..539763b590ea 100644
--- a/pkgs/by-name/un/uni/package.nix
+++ b/pkgs/by-name/un/uni/package.nix
@@ -6,16 +6,16 @@
 
 buildGoModule (finalAttrs: {
   pname = "uni";
-  version = "2.9.0";
+  version = "2.10.0";
 
   src = fetchFromGitHub {
     owner = "arp242";
     repo = "uni";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-+n+QExNCk5QsavO0Kj/e12v4xFJDnXprJGjyk2i/ioY=";
+    hash = "sha256-j7uqxXDFCBbLLOVGKlUEsDdryGkZ6n08E4jZgWtCwJs=";
   };
 
-  vendorHash = "sha256-8nl7iFMmoGuC3pEVi6HqXdwFCKvCDi3DMwRQFjfBC7Y=";
+  vendorHash = "sha256-Jox5uuQactffBJDDxhlCWKzPh0fKL7bLh22ARJBgSII=";
 
   ldflags = [
     "-s"
diff --git a/pkgs/by-name/ur/urn-timer/package.nix b/pkgs/by-name/ur/urn-timer/package.nix
index ceacb81c3acf..2c7bd7990f4c 100644
--- a/pkgs/by-name/ur/urn-timer/package.nix
+++ b/pkgs/by-name/ur/urn-timer/package.nix
@@ -49,5 +49,6 @@ stdenv.mkDerivation {
     license = lib.licenses.gpl3Plus;
     maintainers = with lib.maintainers; [ fgaz ];
     mainProgram = "urn-gtk";
+    platforms = lib.platforms.linux;
   };
 }
diff --git a/pkgs/by-name/vg/vgm2x/package.nix b/pkgs/by-name/vg/vgm2x/package.nix
index cae08d43f195..248ceaed33ba 100644
--- a/pkgs/by-name/vg/vgm2x/package.nix
+++ b/pkgs/by-name/vg/vgm2x/package.nix
@@ -52,6 +52,8 @@ stdenv.mkDerivation (finalAttrs: {
   };
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "VGM file extraction tools";
     homepage = "https://github.com/vampirefrog/vgm2x";
     license = lib.licenses.gpl3Only;
diff --git a/pkgs/by-name/vo/vorta/package.nix b/pkgs/by-name/vo/vorta/package.nix
index f61d71b3168d..8544968dfcb2 100644
--- a/pkgs/by-name/vo/vorta/package.nix
+++ b/pkgs/by-name/vo/vorta/package.nix
@@ -12,14 +12,14 @@
 
 python3Packages.buildPythonApplication (finalAttrs: {
   pname = "vorta";
-  version = "0.11.5";
+  version = "0.11.6";
   pyproject = true;
 
   src = fetchFromGitHub {
     owner = "borgbase";
     repo = "vorta";
     tag = "v${finalAttrs.version}";
-    hash = "sha256-6WY1UAB5Vr+5Az6UYq2DwXwjabcQr7A3QAEQ2/aIzfg=";
+    hash = "sha256-7vV4jv8Gy+viZhQmWECJ02VjoWGWDKTMnzrYkA60OzE=";
   };
 
   nativeBuildInputs = [
diff --git a/pkgs/by-name/wi/wiki-go/package.nix b/pkgs/by-name/wi/wiki-go/package.nix
index d7a76963fd98..2c49239dac4f 100644
--- a/pkgs/by-name/wi/wiki-go/package.nix
+++ b/pkgs/by-name/wi/wiki-go/package.nix
@@ -6,13 +6,13 @@
 
 buildGoModule rec {
   pname = "wiki-go";
-  version = "1.9.0";
+  version = "1.9.1";
 
   src = fetchFromGitHub {
     owner = "leomoon-studios";
     repo = "wiki-go";
     tag = "v${version}";
-    hash = "sha256-kDNPAdvEFdq7uivdd6UsyshZBUDHVKL4Q0pEe3uepbM=";
+    hash = "sha256-QjeDlUznPKW6Uqlqzlkua3RB9PDTL36VHwUKDaNNj5s=";
   };
 
   vendorHash = null;
diff --git a/pkgs/by-name/xs/xsnow/package.nix b/pkgs/by-name/xs/xsnow/package.nix
index 6a6246af0c6c..6f7518c2eb67 100644
--- a/pkgs/by-name/xs/xsnow/package.nix
+++ b/pkgs/by-name/xs/xsnow/package.nix
@@ -42,6 +42,8 @@ stdenv.mkDerivation (finalAttrs: {
   enableParallelBuilding = true;
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "X-windows application that will let it snow on the root, in between and on windows";
     mainProgram = "xsnow";
     homepage = "https://ratrabbit.nl/ratrabbit/xsnow/";
diff --git a/pkgs/by-name/ze/zee/package.nix b/pkgs/by-name/ze/zee/package.nix
index 8d9a9f0c382f..903e82a6fad9 100644
--- a/pkgs/by-name/ze/zee/package.nix
+++ b/pkgs/by-name/ze/zee/package.nix
@@ -4,6 +4,7 @@
   fetchFromGitHub,
   pkg-config,
   openssl,
+  stdenv, # for meta.broken
 }:
 
 rustPlatform.buildRustPackage (finalAttrs: {
@@ -34,6 +35,8 @@ rustPlatform.buildRustPackage (finalAttrs: {
   env.ZEE_DISABLE_GRAMMAR_BUILD = 1;
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "Modern text editor for the terminal written in Rust";
     homepage = "https://github.com/zee-editor/zee";
     license = lib.licenses.mit;
diff --git a/pkgs/by-name/zo/zotero/package.nix b/pkgs/by-name/zo/zotero/package.nix
index 679a1cdd8a2b..779e5584d418 100644
--- a/pkgs/by-name/zo/zotero/package.nix
+++ b/pkgs/by-name/zo/zotero/package.nix
@@ -33,14 +33,14 @@ let
   nodejs = nodejs_22;
 
   pname = "zotero";
-  version = "10.0.1";
+  version = "10.0.2";
 
   src = fetchFromGitHub {
     owner = "zotero";
     repo = "zotero";
     tag = version;
     fetchSubmodules = true;
-    hash = "sha256-ySFz91WD1KW2V0PETnMQLPm8Og69nbvlpmkf0PHWTQQ=";
+    hash = "sha256-V0dYKFWr1ZjYNEWufslW/NqfjPZOb8W1pECz33PcCEQ=";
   };
 
   pdf-js = buildNpmPackage {
diff --git a/pkgs/development/interpreters/erlang/29.nix b/pkgs/development/interpreters/erlang/29.nix
index ef7fc237d9a0..a40c8cc08ea8 100644
--- a/pkgs/development/interpreters/erlang/29.nix
+++ b/pkgs/development/interpreters/erlang/29.nix
@@ -1,6 +1,6 @@
 genericBuilder:
 
 genericBuilder {
-  version = "29.0.6";
-  hash = "sha256-k5AsIz5c86XP2lA/MF9NwEJ5hD5Ln/uHqZvjhhsHBwI=";
+  version = "29.1";
+  hash = "sha256-G1YZCdaicgmuZYXIi6g5bRM4nkvJoLb7fGdBCD+NIvQ=";
 }
diff --git a/pkgs/development/lua-modules/generated-packages.nix b/pkgs/development/lua-modules/generated-packages.nix
index bf97d961b2e0..f71a99893861 100644
--- a/pkgs/development/lua-modules/generated-packages.nix
+++ b/pkgs/development/lua-modules/generated-packages.nix
@@ -4607,7 +4607,7 @@ final: prev: {
       meta = {
         homepage = "https://github.com/horriblename/lzn-auto-require";
         maintainers = with lib.maintainers; [ mrcjkb ];
-        license.fullName = "GPL-2.0";
+        license = lib.licenses.gpl2Only;
         description = "Auto load optional plugins via lua modules with lz.n";
       };
     }
diff --git a/pkgs/development/misc/msp430/mspds/default.nix b/pkgs/development/misc/msp430/mspds/default.nix
index 553fdec3fd96..e6630aa464d0 100644
--- a/pkgs/development/misc/msp430/mspds/default.nix
+++ b/pkgs/development/misc/msp430/mspds/default.nix
@@ -66,6 +66,8 @@ stdenv.mkDerivation {
   ++ lib.optional stdenv.hostPlatform.isLinux libusb1;
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "TI MSP430 FET debug driver";
     homepage = "https://www.ti.com/tool/MSPDS";
     license = lib.licenses.bsd3;
diff --git a/pkgs/development/python-modules/compressed-tensors/default.nix b/pkgs/development/python-modules/compressed-tensors/default.nix
index 2c143c869b5c..b16dc1460297 100644
--- a/pkgs/development/python-modules/compressed-tensors/default.nix
+++ b/pkgs/development/python-modules/compressed-tensors/default.nix
@@ -25,7 +25,7 @@
 
 buildPythonPackage (finalAttrs: {
   pname = "compressed-tensors";
-  version = "0.17.1";
+  version = "0.18.0";
   pyproject = true;
 
   # Release on PyPI is missing the `utils` directory, which `setup.py` wants to import
@@ -33,7 +33,7 @@ buildPythonPackage (finalAttrs: {
     owner = "neuralmagic";
     repo = "compressed-tensors";
     tag = finalAttrs.version;
-    hash = "sha256-14AHbokDlN5iXy/fvOq7Xp1OS8N1b+Xpxd33KOylWiU=";
+    hash = "sha256-cbHP2YZgG0UY+rrcOKKwtgwga2pEZaEEMoJqq57pFb0=";
   };
 
   postPatch = ''
@@ -132,6 +132,8 @@ buildPythonPackage (finalAttrs: {
   disabledTestPaths = [
     # these try to download models from HF Hub
     "tests/test_quantization/lifecycle/test_apply.py"
+    "tests/test_quantization/test_quant_config.py::test_map_to_checkpoint_names"
+
     # RuntimeError: The weights trying to be saved contained shared tensors
     "tests/test_transform/factory/test_serialization.py::test_serialization[True-hadamard]"
     "tests/test_transform/factory/test_serialization.py::test_serialization[True-random-hadamard]"
@@ -153,6 +155,11 @@ buildPythonPackage (finalAttrs: {
     "tests/test_compressors/distributed/test_module_parallel.py"
     "tests/test_compressors/model_compressors/test_model_compressor_distributed.py"
     "tests/test_offload"
+    # https://github.com/vllm-project/compressed-tensors/issues/885
+    "tests/test_compressors/model_compressors/test_model_compressor.py"
+
+    # Tests require CUDA
+    "tests/test_compressors/test_compress_decompress_module.py"
   ]
   ++ lib.optionals stdenv.hostPlatform.isDarwin [
     # AssertionError: Torch not compiled with CUDA enabled
diff --git a/pkgs/development/python-modules/cyvcf2/default.nix b/pkgs/development/python-modules/cyvcf2/default.nix
new file mode 100644
index 000000000000..a29f7f21b2b7
--- /dev/null
+++ b/pkgs/development/python-modules/cyvcf2/default.nix
@@ -0,0 +1,89 @@
+{
+  lib,
+  buildPythonPackage,
+  fetchFromGitHub,
+  python,
+
+  # build-system
+  cmake,
+  cython,
+  ninja,
+  numpy,
+  scikit-build-core,
+
+  # nativeBuildInputs
+  pkg-config,
+
+  # buildInputs
+  htslib,
+
+  # dependencies
+  click,
+  coloredlogs,
+
+  # tests
+  pytestCheckHook,
+}:
+
+buildPythonPackage (finalAttrs: {
+  pname = "cyvcf2";
+  version = "0.34.0";
+  pyproject = true;
+  __structuredAttrs = true;
+
+  src = fetchFromGitHub {
+    owner = "brentp";
+    repo = "cyvcf2";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-XDo2cEcZm5y6u9Gc2e7q2tg8pt3C/5cmnWRe6Dr5x7M=";
+  };
+
+  build-system = [
+    cmake
+    cython
+    ninja
+    numpy
+    scikit-build-core
+  ];
+  dontUseCmakeConfigure = true;
+
+  nativeBuildInputs = [
+    pkg-config
+  ];
+
+  buildInputs = [
+    htslib
+  ];
+
+  env = {
+    # Link against the system htslib instead of building the bundled submodule
+    CYVCF2_HTSLIB_MODE = "EXTERNAL";
+  };
+
+  dependencies = [
+    click
+    coloredlogs
+    numpy
+  ];
+
+  pythonImportsCheck = [ "cyvcf2" ];
+
+  nativeCheckInputs = [
+    pytestCheckHook
+  ];
+
+  # The test suite lives inside the package directory and relies on relative imports
+  # (`from ..cyvcf2 import VCF`) as well as data files next to it, so it must run from the source
+  # tree. Bring the compiled extension along.
+  preCheck = ''
+    cp $out/${python.sitePackages}/cyvcf2/cyvcf2*.so cyvcf2/
+  '';
+
+  meta = {
+    description = "Cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files";
+    homepage = "https://github.com/brentp/cyvcf2";
+    changelog = "https://github.com/brentp/cyvcf2/blob/${finalAttrs.src.rev}/CHANGES.md";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ GaetanLepage ];
+  };
+})
diff --git a/pkgs/development/python-modules/pybedtools/default.nix b/pkgs/development/python-modules/pybedtools/default.nix
new file mode 100644
index 000000000000..44d71233a1df
--- /dev/null
+++ b/pkgs/development/python-modules/pybedtools/default.nix
@@ -0,0 +1,100 @@
+{
+  lib,
+  stdenv,
+  buildPythonPackage,
+  fetchFromGitHub,
+  python,
+
+  # build-system
+  cython,
+  setuptools,
+
+  # buildInputs
+  zlib,
+
+  # dependencies
+  bedtools,
+  numpy,
+  pandas,
+  pysam,
+
+  # tests
+  psutil,
+  pytestCheckHook,
+  pyyaml,
+}:
+buildPythonPackage (finalAttrs: {
+  pname = "pybedtools";
+  version = "0.12.1";
+  pyproject = true;
+  __structuredAttrs = true;
+
+  src = fetchFromGitHub {
+    owner = "daler";
+    repo = "pybedtools";
+    tag = "v${finalAttrs.version}";
+    hash = "sha256-s+MSiNtGwR7Gshka7NeBE+OnHiht1R6xh4Sx8/0wfS0=";
+  };
+
+  postPatch =
+    # `pybedtools` shells out to the BEDTools executables. Hardcode their location
+    # instead of relying on them being present in `PATH`.
+    ''
+      substituteInPlace pybedtools/settings.py \
+        --replace-fail \
+          '_bedtools_path = ""' \
+          '_bedtools_path = "${lib.getBin bedtools}/bin"'
+    '';
+
+  build-system = [
+    cython
+    setuptools
+  ];
+
+  buildInputs = [
+    zlib
+  ];
+
+  dependencies = [
+    numpy
+    pandas
+    pysam
+  ];
+
+  pythonImportsCheck = [ "pybedtools" ];
+
+  nativeCheckInputs = [
+    bedtools
+    psutil
+    pytestCheckHook
+    pyyaml
+  ];
+
+  # The package ships compiled extension modules, so run the test suite against
+  # the installed copy rather than the source tree.
+  preCheck = ''
+    cd $out/${python.sitePackages}
+  '';
+
+  enabledTestPaths = [ "pybedtools/test" ];
+
+  disabledTests = [
+    # Requires internet access
+    "test_chromsizes"
+
+    # FileNotFoundError: [Errno 2] No such file or directory: '/bin/bash'
+    "test_issue_303"
+  ]
+  ++ lib.optionals stdenv.hostPlatform.isDarwin [
+    # AssertionError: assert '' == 'chr1\t1\t100...ture4\t0\t+\n'
+    "test_all"
+  ];
+
+  meta = {
+    description = "Wrapper around BEDTools for bioinformatics work";
+    homepage = "https://github.com/daler/pybedtools";
+    changelog = "https://github.com/daler/pybedtools/releases/tag/${finalAttrs.src.tag}";
+    license = lib.licenses.mit;
+    maintainers = with lib.maintainers; [ GaetanLepage ];
+  };
+})
diff --git a/pkgs/tools/security/ghidra/extensions/gnudisassembler/default.nix b/pkgs/tools/security/ghidra/extensions/gnudisassembler/default.nix
index 3e6246f35865..b168f846812f 100644
--- a/pkgs/tools/security/ghidra/extensions/gnudisassembler/default.nix
+++ b/pkgs/tools/security/ghidra/extensions/gnudisassembler/default.nix
@@ -64,6 +64,8 @@ buildGhidraExtension {
   '';
 
   meta = {
+    # last successful hydra build on darwin was in 2024
+    broken = stdenv.hostPlatform.isDarwin;
     description = "Leverage the binutils disassembler capabilities for various processors";
     homepage = "https://ghidra-sre.org/";
     downloadPage = "https://github.com/NationalSecurityAgency/ghidra/tree/master/GPL/GnuDisassembler";
diff --git a/pkgs/top-level/aliases.nix b/pkgs/top-level/aliases.nix
index f6a1f7348b8b..d17ec2a2ef79 100644
--- a/pkgs/top-level/aliases.nix
+++ b/pkgs/top-level/aliases.nix
@@ -2321,6 +2321,7 @@ mapAliases {
   signal-desktop-source = throw "'signal-desktop-source' has been renamed to/replaced by 'signal-desktop'"; # Converted to throw 2025-10-27
   silver-searcher = throw "'silver-searcher' has been removed as it has seen no development since 2020 and is stuck on the obsolete pcre library. Consider using 'silver-searcher-ng', which is a fork with support for PCRE2.";
   simple64-netplay-server = gopher64-netplay-server; # Added 2026-08-01
+  simple-mtpfs = throw "'simple-mtpfs has been removed because it is unmaintained upstream.'"; # Added 2026-07-30
   simpleBluez = warnAlias "'simpleBluez' has been renamed to 'simplebluez'" simplebluez; # Added 2026-02-18
   simpleDBus = warnAlias "'simpleDBus' has been renamed to 'simpledbus'" simpledbus; # Added 2026-02-12
   simplesamlphp = throw "'simplesamlphp' was removed because it was unmaintained in nixpkgs"; # Added 2025-10-17
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 48124b9b9cce..38c9e74c71e9 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -3983,6 +3983,8 @@ self: super: with self; {
 
   cytoolz = callPackage ../development/python-modules/cytoolz { };
 
+  cyvcf2 = callPackage ../development/python-modules/cyvcf2 { };
+
   cyvest = callPackage ../development/python-modules/cyvest { };
 
   dacite = callPackage ../development/python-modules/dacite { };
@@ -14507,6 +14509,8 @@ self: super: with self; {
 
   pybcj = callPackage ../development/python-modules/pybcj { };
 
+  pybedtools = callPackage ../development/python-modules/pybedtools { };
+
   pybids = callPackage ../development/python-modules/pybids { };
 
   pybigwig = callPackage ../development/python-modules/pybigwig { };