v4.0.0: codec 2.60.4 security release, --pq-box sealed-box mode, F-16 fix

Major release. Highlights:

- Codec: vendored VaptVupt codec moves to canonical 2.60.4 security
  release. Fixes a high-severity OOB heap write in the AVX2 decode fast
  path (reachable on a valid stream sized to exactly content_size, both
  tail variants). Brings CBMC-formally-verified BCJ filters with
  automatic ELF/PE/Mach-O detection. Compressed output stays
  byte-identical (ratio gate Δ 0.00%); wire format unchanged at v1.6.
- New --pq-box sealed-box recipient mode (vendored libpqvaptvupt 0.6.0):
  ML-KEM-768 + X25519 combined via HKDF-SHA256 with domain separation,
  AES-256-CTR + HMAC-SHA256 EtM. Legacy --pq and --pq-sdk stay readable.
- F-16: discloses and fixes a pre-existing data-loss defect in the
  <= 3.8.0 in-tree BCJ encoder. Full back-compat matrix decodes
  byte-exact under 4.0.0; every readable pre-4.0 archive remains readable.

Repository hygiene:
- Sync full 4.0.0 source tree (codec, crypto, SDK, GUI, packaging, tests).
- Remove internal scratch files (PROMPT.md, FORMAL_AUDIT_PROMPT.md)
  and superseded version-specific docs (INTEGRATION_PROTOCOL_2.60.4.md,
  docs/FINDINGS-2.x.md) and a stray test binary.
- Refresh README download/install section to real 4.0.0 release assets;
  bump version badge to 4.0.0.
- Add .gitignore for build outputs (keeps vendored prebuilt libraries).

packaging/nix/flake.nix

@@ -0,0 +1,120 @@
+# SPDX-License-Identifier: AGPL-3.0-or-later
+#
+# Nix flake for zupt.
+#
+# Usage (with flakes enabled):
+#   nix build .#zupt                    # build the package
+#   nix run .#zupt -- version           # run zupt directly
+#   nix develop                         # drop into a dev shell
+#   nix flake check                     # lint the flake
+#
+# To consume from another flake:
+#   inputs.zupt.url = "git+https://git.securityops.co/cristiancmoises/zupt?ref=v2.4.4";
+#   ...packages.x86_64-linux.default = inputs.zupt.packages.x86_64-linux.zupt;
+#
+# Reproducibility:
+#   * Nix already pins the source tree by hash.
+#   * `make dist` is also reproducible (tests/test_dist_reproducible.sh).
+#   * Together, two independent Nix evaluations of the same flake.lock
+#     produce byte-identical /nix/store outputs.
+
+{
+  description = "Zupt — post-quantum backup compression utility (C11)";
+
+  inputs = {
+    nixpkgs.url = "github:NixOS/nixpkgs/nixos-24.11";
+    flake-utils.url = "github:numtide/flake-utils";
+  };
+
+  outputs = { self, nixpkgs, flake-utils }:
+    flake-utils.lib.eachSystem [ "x86_64-linux" "aarch64-linux" ] (system:
+      let
+        pkgs = import nixpkgs { inherit system; };
+
+        zupt = pkgs.stdenv.mkDerivation {
+          pname = "vaptvupt";
+          version = "4.0.0";
+
+          # When publishing, replace this with `fetchurl` against the
+          # release tarball. For local development the flake assumes it
+          # lives in the same directory as the source.
+          src = ./.;
+
+          nativeBuildInputs = with pkgs; [
+            gcc
+            gnumake
+          ];
+
+          # python3 is only used by the regression-test harness.
+          checkInputs = [ pkgs.python3 ];
+
+          # Build with the project's preferred warning set on top of Nix's
+          # hardening flags. Don't override -O2 from stdenv.
+          NIX_CFLAGS_COMPILE = "-Wall -Wextra -Wpedantic -std=c11";
+
+          # `make` builds the binary using vendored libzuptsdk via rpath.
+          buildPhase = ''
+            runHook preBuild
+            make -j$NIX_BUILD_CORES
+            runHook postBuild
+          '';
+
+          # Run the full upstream regression suite. Disable per-package by
+          # setting doCheck = false; on by default.
+          doCheck = true;
+          checkPhase = ''
+            runHook preCheck
+            make test
+            runHook postCheck
+          '';
+
+          installPhase = ''
+            runHook preInstall
+            make DESTDIR=$out PREFIX= install
+
+            # Move libzuptsdk into $out/lib/zupt/. The binary's rpath is
+            # $ORIGIN/../lib/zupt after autopatchelf rewrites it during
+            # the fixup phase.
+            mkdir -p $out/lib/zupt
+            install -m 0755 vendor/zuptsdk/libzuptsdk.so.2.0.0 \
+              $out/lib/zupt/libzuptsdk.so.2.0.0
+            ln -sf libzuptsdk.so.2.0.0 $out/lib/zupt/libzuptsdk.so.2
+            ln -sf libzuptsdk.so.2.0.0 $out/lib/zupt/libzuptsdk.so
+
+            # Docs
+            mkdir -p $out/share/doc/zupt
+            cp README.md SECURITY.md CHANGELOG.md AUDIT.md $out/share/doc/zupt/
+            runHook postInstall
+          '';
+
+          meta = with pkgs.lib; {
+            description = "Post-quantum backup compression utility (ML-KEM-768 + AES-256-CTR + HMAC-SHA256 + Argon2id)";
+            homepage = "https://git.securityops.co/cristiancmoises/zupt";
+            license = with licenses; [ agpl3Plus gpl3Plus ];
+            maintainers = [ ];
+            platforms = [ "x86_64-linux" "aarch64-linux" ];
+            mainProgram = "zupt";
+          };
+        };
+      in {
+        packages = {
+          zupt = zupt;
+          default = zupt;
+        };
+
+        apps.default = {
+          type = "app";
+          program = "${zupt}/bin/zupt";
+        };
+
+        devShells.default = pkgs.mkShell {
+          buildInputs = with pkgs; [
+            gcc
+            gnumake
+            python3
+            valgrind
+            gdb
+          ];
+        };
+      });
+}