- `retroarch` has been refactored and the older `retroarch.override { cores = [ ... ]; }` to create a RetroArch derivation with custom cores doesn't work anymore, use `retroarch.withCores (cores: [ ... ])` instead. If you need more customization (e.g.: custom settings), use `wrapRetroArch` instead.

- `borgmatic` has been updated from 1.8.14 to 1.9.5, please check the [upstream changelog](https://projects.torsion.org/borgmatic-collective/borgmatic/releases) for more details, especially for a few possibly breaking changes noted in the [1.9.0 changelog](https://projects.torsion.org/borgmatic-collective/borgmatic/releases/tag/1.9.0).

- `nodePackages.ganache` has been removed, as the package has been deprecated by upstream.

- `matomo` now defaults to version 5 (previously available as `matomo_5`). Version 4 has been removed as it reached EOL on December 19, 2024.

- `matomo-beta` has been removed as the version of the `matomo` package can now be easily overridden through `overrideAttrs` (see [PR #374022](https://github.com/NixOS/nixpkgs/pull/374022))

- `docker_24` has been removed, as it was EOL with vulnerabilities since June 08, 2024.

- Emacs 28 and 29 have been removed.

- Emacs 28 Macport has been removed, while CVEs of Emacs 29 Macport are patched.

- `containerd` has been updated to v2, which contains breaking changes. See the [containerd
  2.0](https://github.com/containerd/containerd/blob/main/docs/containerd-2.0.md) documentation for more
  details.

- The `tinycc` package now has the `dev`, `doc` and `lib` outputs, thus,
`tinycc.out` may now only provide the tcc and cross compilers binaries.

- The `testTarget` argument of `haskellPackages.mkDerivation` has been deprecated in favour of `testTargets`.
  `testTarget` took a space separated string of targets, whereas the new `testTargets` argument takes a list of targets.
  For instance, `testTarget = "foo bar baz"` should become `testTargets = [ "foo" "bar" "baz" ]`.

- `rustPlatform.buildRustPackage` stops handling the deprecated argument `cargoSha256`. Out-of-tree packages that haven't migrated from `cargoSha256` to `cargoHash` now receive errors.

- `nodePackages.stackdriver-statsd-backend` has been removed, as the StackDriver service has been discontinued by Google, and therefore the package no longer works.

- `python3Packages.opentracing` has been removed due to being unmaintained upstream. [OpenTelemetry](https://opentelemetry.io/) is the recommended replacement.

- the notmuch vim plugin now lives in a separate output of the `notmuch`
  package. Installing `notmuch` will not bring the notmuch vim package anymore,
  add `vimPlugins.notmuch-vim` to your (Neo)vim configuration if you want the
  vim plugin.

- The fileSystems (e.g., `fileSystems."/"`) are now set by NixOS-implemented modules using `lib.mkDefault`, allowing wholesale overrides, but this means that overriding individual attributes (like `fsType` or `options`) without explicitly specifying `device` may result in missing required fields and errors such as `No device specified for mount point '/'` (https://github.com/NixOS/nixpkgs/pull/377406).

- `prisma` and `prisma-engines` have been updated to version 6.7.0, which
  introduces several breaking changes. See the
  [Prisma ORM upgrade guide](https://www.prisma.io/docs/orm/more/upgrade-guides/upgrading-versions/upgrading-to-prisma-6)
  for more information.

- `dependency-track` no longer bundles the UI inside the jar. This bundling
  functionality is deprecated by upstream and causes UI assets not being served
  after weeks of runtime.

- `nq` was updated to 1.0, which renames the `fq` and `tq` utilities to `nqtail` and `nqterm` respectively.

- `zf` was updated to 0.10.2, which includes breaking changes from the [0.10.0 release](https://github.com/natecraddock/zf/releases/tag/0.10.0).
  `zf` no longer does Unicode normalization of the input and no longer supports terminal escape sequences in the `ZF_PROMPT` environment variable.

- `confluent-cli` was updated from 3.60.0 to 4.16.0, which includes several breaking changes as detailed in [Confluent's release notes](https://docs.confluent.io/confluent-cli/current/release-notes.html).