Clean up overlays and remove obsolete dependencies

overlays/patches/README.md

@@ -0,0 +1,46 @@
+# Package patches
+
+Each package follows the [GnuTLS layout](gnutls/README.md):
+
+- `default.nix` applies the patch through the package overlay.
+- A descriptive `.patch` file contains the standalone upstream source change.
+- `README.md` explains the problem, scope, reproduction, upstream status,
+  Nix integration, and recorded validation limits.
+- Companion `verify-*` tools live beside the patch when needed; otherwise
+  the README gives commands for the package's existing tests.
+
+Keep package-specific evidence in its directory. Patch headers explain the
+change independently of Nix, and `default.nix` preserves existing patches.
+
+| Package | Repair |
+| --- | --- |
+| [Abseil](abseil/README.md) | Public BMI2 header in Electron, Deno, and Signal's vendored copies |
+| [Backrefs](backrefs/README.md) | Match the regex timeout's CPU clock |
+| [GnuTLS](gnutls/README.md) | Wait for the UDP server socket before connecting |
+| [Jupyter Server](jupyter-server/README.md) | Exercise the correct shared future during reconnect |
+| [Prometheus](prometheus/README.md) | Complete parsing before inspecting the test editor state |
+| [pytest-xdist](pytest-xdist/README.md) | Check worker replacements despite concurrent crashes |
+| [SciPy](scipy/README.md) | Account for floating-point rounding in STFT tests |
+| [Sentry SDK](sentry-sdk/README.md) | Isolate SDK thread mocks from Python's threading module |
+| [Torchaudio](torchaudio/README.md) | Compare pitch-shift batches at appropriate precision |
+| [TorchCodec](torchcodec/README.md) | Match the reference MP3 encoder's sample format |
+
+## Local NixOS integration
+
+[`../default.nix`](../default.nix) imports this directory's
+[`default.nix`](default.nix), which wires each package's override into the
+package set. Abseil repairs several vendored copies and is gated on
+`x86-64-v3`; Prometheus patches its separate assets derivation; Python
+packages use `pythonPackagesExtensions`.
+
+[`../test-exclusions.nix`](../test-exclusions.nix) retains only pytest-xdist's
+outer-worker limit and inner-worker startup allowance. It adds no skipped
+tests. Existing nixpkgs exclusions remain separate from these repairs.
+
+The test-exclusion review used Python 3.14.7 and the pinned x86-64-v3 package
+set. Host-flake evaluation verified patch wiring, Python install checks,
+removal of the local skips, and Prometheus's reference to the patched assets.
+Jupyter and Sentry package tests used the preceding dependency set with the
+new package patch to avoid unrelated rebuilds after pytest-xdist changed.
+No complete NixOS rebuild was performed. Individual READMEs distinguish
+package builds, focused tests, and checks that have not been run.