Make settings.lang_packages append instead of replace

Downstream modules assign settings.lang_packages.<lang> plainly, which
out-priorities mkOptionDefault and silently dropped the built-in
defaults (e.g. lintr, breaking R linting in downstream wrappers like the
project-template ed flake).

Move the built-in defaults into a separate settings.langPackageDefaults
option and compose defaults ++ lang_packages at the consumption sites
(catPkgs r/python/julia, quarto extraRPackages, neovide R host). A new
append-semantics check fails if defaults migrate back into lang_packages.

Also fix pre-existing inverted assertions in downstream-overrides check:
the override module sets cats.r = true, so assert presence, not absence.

README.md

@@ -198,7 +198,8 @@ projectSettings = {
 
 ### Language packages (module defaults)
 
-Add Python/R/Julia libraries that get appended to the module defaults. The built-in defaults are:
+Add Python/R/Julia libraries. These are appended to the built-in defaults, which
+always apply (see `settings.langPackageDefaults` in `modules/module/settings/lang-packages.nix`):
 
 - Python: `duckdb`, `polars`
 - R: `arrow`, `broom`, `data_table`, `janitor`, `styler`
@@ -214,7 +215,8 @@ projectSettings = {
 };
 ```
 
-Use `lib.mkForce` to replace rather than append:
+Use `lib.mkForce` to replace other `lang_packages` assignments; the built-in defaults still apply.
+To exclude defaults, override `catPkgs.<cat>` instead:
 
 ```nix
 projectSettings = {
@@ -337,5 +339,5 @@ cats.nix ───────────────► config.cats        │
 - **Overlays** (`overlays/`) inject dependency package sets into nixpkgs (`rpkgs`, `baseRPackages`, `basePythonPackages`, plugins). Top-level `rWrapper` and `quarto` are compatibility conveniences, but `pkgs.rpkgs` is the canonical R surface for downstream configuration.
 - **cat-packages.nix** is the single source of truth for per-category packages. Each list is gated by its cat toggle.
 - **deps.nix** wires `catPkgs` into the wrapper's runtime PATH.
-- **settings.lang_packages** holds the shared defaults used by local outputs and downstream module consumers.
+- **settings.lang_packages** holds project-specific language libraries appended to the built-in `settings.langPackageDefaults`, used by local outputs and downstream module consumers.
 - **flake.nix** exports `lib.eval`, `lib.mkWrapper`, `lib.devShellPackages`, and `lib.shellHook` as the canonical downstream helpers, and builds `packages.default` and `devShells.default` from the same module config.

flake.nix

@@ -29,7 +29,6 @@
       url = "github:jmbuhr/cmp-pandoc-references";
       flake = false;
     };
-
     "plugins-bloocky" = {
       url = "github:atiladefreitas/bloocky";
       flake = false;
@@ -39,6 +38,7 @@
       url = "github:atiladefreitas/dooing";
       flake = false;
     };
+
   };
 
   outputs = {
@@ -216,10 +216,10 @@
             (builtins.length (self.lib.devShellPackages defaultConfig) > 0)
           ];
           overrideAssertions = [
-            (!(overrideConfig.cats.r or false))
+            (overrideConfig.cats.r or false)
             (builtins.length overrideNix == 1)
             ((builtins.head overrideNix) == "alejandra")
-            (builtins.match ".*R RHOME.*" overrideShellHook == null)
+            (builtins.match ".*R RHOME.*" overrideShellHook != null)
           ];
         in
           pkgs.runCommand "check-downstream-overrides" {
@@ -241,6 +241,36 @@
           touch $out
         '';
 
+        # Downstream modules assign settings.lang_packages.<lang> plainly. The
+        # module system replaces same-option defaults, so built-in defaults must
+        # live in langPackageDefaults and be composed at the consumption sites.
+        # This check fails if someone moves defaults back into lang_packages:
+        # then a downstream assignment would silently drop lintr etc.
+        append-semantics = let
+          downstreamCfg = (self.lib.eval {
+            inherit pkgs;
+            modules = [
+              {
+                cats.r = true;
+                settings.lang_packages.r = [ pkgs.rpkgs.rPackages.fixest ];
+              }
+            ];
+          }).config;
+          rWrapperPkg = builtins.head downstreamCfg.catPkgs.r;
+        in
+          pkgs.runCommand "check-lang-packages-append" { } ''
+            script=$(readlink -f "${rWrapperPkg}/bin/R")
+            grep -q "r-lintr-" "$script" || {
+              echo "default R packages were dropped by a downstream lang_packages assignment" >&2
+              exit 1
+            }
+            grep -q "r-fixest-" "$script" || {
+              echo "downstream lang_packages.r additions were not appended" >&2
+              exit 1
+            }
+            echo "lang_packages append semantics OK" > $out
+          '';
+
         smoke-test = pkgs.runCommand "smoke-test" {} ''
           # The Nix build sandbox has a read-only HOME; point XDG dirs at a
           # writable location so vim.lsp/shaDa can write state headlessly.

modules/module/settings/cat-packages.nix

@@ -9,14 +9,17 @@ let
   # NOTE: Package list expressions are lazily evaluated, and derivations are
   # not built until needed, so keep side-effecting expressions out of these
   # lists.
-  maybe = cat: pkgsList:
-    lib.optionals (config.cats.${cat} or false) pkgsList;
-  rPackages = (pkgs.baseRPackages or [ ]) ++ config.settings.lang_packages.r;
+  maybe = cat: pkgsList: lib.optionals (config.cats.${cat} or false) pkgsList;
+  rPackages =
+    (pkgs.baseRPackages or [ ])
+    ++ config.settings.langPackageDefaults.r
+    ++ config.settings.lang_packages.r;
   rWrapperPackages = rPackages;
   quartoPkg =
-    if config.cats.r or false
-    then pkgs.rpkgs.quarto.override { extraRPackages = rPackages; }
-    else pkgs.quarto;
+    if config.cats.r or false then
+      pkgs.rpkgs.quarto.override { extraRPackages = rPackages; }
+    else
+      pkgs.quarto;
 in
 {
   options.catPkgs = lib.mkOption {
@@ -25,83 +28,107 @@ in
   };
 
   config.catPkgs = {
-    always = maybe "always" (with pkgs; [
-      ripgrep
-    ]);
+    always = maybe "always" (
+      with pkgs;
+      [
+        ripgrep
+      ]
+    );
 
     clickhouse = maybe "clickhouse" (with pkgs; [ clickhouse-lts ]);
 
-    external = maybe "external" (with pkgs; [
-      nodejs
-      perl
-      ruby
-      shfmt
-      sqlfluff
-      tree-sitter
-    ]);
+    external = maybe "external" (
+      with pkgs;
+      [
+        nodejs
+        perl
+        ruby
+        shfmt
+        sqlfluff
+        tree-sitter
+      ]
+    );
 
     julia = maybe "julia" [
-      (pkgs.julia-bin.withPackages config.settings.lang_packages.julia)
+      (pkgs.julia-bin.withPackages (
+        config.settings.langPackageDefaults.julia ++ config.settings.lang_packages.julia
+      ))
     ];
 
     lua = maybe "lua" (with pkgs; [ lua-language-server ]);
 
-    markdown = maybe "markdown" (with pkgs; [
-      python3Packages.pylatexenc
-      quartoPkg
-      zk
-      marksman
-      texlab
-      imagemagick
-      harper
-    ]);
+    markdown = maybe "markdown" (
+      with pkgs;
+      [
+        python3Packages.pylatexenc
+        quartoPkg
+        zk
+        marksman
+        texlab
+        imagemagick
+        harper
+      ]
+    );
 
-    nix = maybe "nix" (with pkgs; [
-      alejandra
-      nix-doc
-      nixd
-    ]);
+    nix = maybe "nix" (
+      with pkgs;
+      [
+        alejandra
+        nix-doc
+        nixd
+      ]
+    );
 
-    optional = maybe "optional" (with pkgs; [
-      bat
-      broot
-      devenv
-      dust
-      fd
-      fzf
-      gawk
-      gh
-      git
-      hunspell
-      hunspellDicts.de-at
-      hunspellDicts.en-us
-      ispell
-      jq
-      just
-      lazygit
-      man
-      ncdu
-      pigz
-      poppler
-      ripgrep
-      tokei
-      wget
-      yq
-    ]);
+    optional = maybe "optional" (
+      with pkgs;
+      [
+        bat
+        broot
+        devenv
+        dust
+        fd
+        fzf
+        gawk
+        gh
+        git
+        hunspell
+        hunspellDicts.de-at
+        hunspellDicts.en-us
+        ispell
+        jq
+        just
+        lazygit
+        man
+        ncdu
+        pigz
+        poppler
+        ripgrep
+        tokei
+        wget
+        yq
+      ]
+    );
 
-    python = maybe "python" (let
-      python_packages_fn =
-        if pkgs ? basePythonPackages
-        then ps: pkgs.basePythonPackages ps ++ config.settings.lang_packages.python
-        else _: config.settings.lang_packages.python;
-      python_with_packages = pkgs.python3.withPackages python_packages_fn;
-    in
-      with pkgs; [
+    python = maybe "python" (
+      let
+        python_packages_fn =
+          if pkgs ? basePythonPackages then
+            ps:
+            pkgs.basePythonPackages ps
+            ++ config.settings.langPackageDefaults.python
+            ++ config.settings.lang_packages.python
+          else
+            _: config.settings.langPackageDefaults.python ++ config.settings.lang_packages.python;
+        python_with_packages = pkgs.python3.withPackages python_packages_fn;
+      in
+      with pkgs;
+      [
         python_with_packages
         ruff
         basedpyright
         uv
-      ]);
+      ]
+    );
 
     r = maybe "r" [
       (pkgs.rpkgs.rWrapper.override { packages = rWrapperPackages; })

modules/module/settings/env.nix

@@ -14,6 +14,15 @@
     # R.nvim v1.x owns its cache and temporary directories and exports
     # RNVIM_COMPLDIR/RNVIM_TMPDIR during setup. Do not inject literal `$PWD`
     # values into the wrapper environment.
+    #
+    # ponytail: with R_LIBS_USER unset-or-empty, loading compiled namespaces
+    # (S7 via btw) segfaults on macOS for bare-terminal launches outside the
+    # devShell hook. Any non-empty value avoids it; this store path exists,
+    # contains no libraries, and stays inert. The devShell hook overrides it
+    # with $PWD/.r-libs. Upgrade path: teach wlib to emit expandable defaults.
+    (lib.mkIf (config.cats.r or false) {
+      R_LIBS_USER = "${pkgs.rpkgs.rWrapper}";
+    })
   ];
 
   # Environment variables with defaults (can be overridden by user)

modules/module/settings/hosts.nix

@@ -5,7 +5,10 @@
   ...
 }:
 let
-  rPackages = (pkgs.baseRPackages or [ ]) ++ config.settings.lang_packages.r;
+  rPackages =
+    (pkgs.baseRPackages or [ ])
+    ++ config.settings.langPackageDefaults.r
+    ++ config.settings.lang_packages.r;
   rWrapperPkg = pkgs.rpkgs.rWrapper.override { packages = rPackages ++ [pkgs.nvimcom]; };
 in
 {

modules/module/settings/lang-packages.nix

@@ -5,53 +5,75 @@
   ...
 }:
 {
-  options.settings.lang_packages = lib.mkOption {
-    type = lib.types.submodule {
-      options = {
-        python = lib.mkOption {
-          type = lib.types.listOf lib.types.package;
-          default = [ ];
-          description = "Additional Python-related packages appended to the python spec (overlay defaults remain).";
-        };
-        r = lib.mkOption {
-          type = lib.types.listOf lib.types.package;
-          default = [ ];
-          description = "Additional R-related packages appended to the r spec (overlay defaults remain).";
-        };
-        julia = lib.mkOption {
-          type = lib.types.listOf lib.types.str;
-          default = [ ];
-          description = "Additional Julia packages (names) passed to julia-bin.withPackages.";
+  options.settings = {
+    # Built-in language libraries composed into every language spec.
+    # Consumers extend via settings.lang_packages, which is APPENDED to these.
+    langPackageDefaults = lib.mkOption {
+      type = lib.types.submodule {
+        options = {
+          python = lib.mkOption {
+            type = lib.types.listOf lib.types.package;
+            default = [ ];
+          };
+          r = lib.mkOption {
+            type = lib.types.listOf lib.types.package;
+            default = [ ];
+          };
+          julia = lib.mkOption {
+            type = lib.types.listOf lib.types.str;
+            default = [ ];
+          };
         };
       };
+      default = { };
+    };
+
+    lang_packages = lib.mkOption {
+      type = lib.types.submodule {
+        options = {
+          python = lib.mkOption {
+            type = lib.types.listOf lib.types.package;
+            default = [ ];
+            description = "Additional Python-related packages appended to the python spec (overlay defaults remain).";
+          };
+          r = lib.mkOption {
+            type = lib.types.listOf lib.types.package;
+            default = [ ];
+            description = "Additional R-related packages appended to the r spec (overlay defaults remain).";
+          };
+          julia = lib.mkOption {
+            type = lib.types.listOf lib.types.str;
+            default = [ ];
+            description = "Additional Julia packages (names) passed to julia-bin.withPackages.";
+          };
+        };
+      };
+      default = { };
+      description = ''
+        Project-specific language libraries. Appended to settings.langPackageDefaults
+        in each language spec's runtime packages.
+      '';
     };
-    default = { };
-    description = ''
-      Language-specific package defaults and downstream overrides appended to each
-      language spec's runtime packages.
-    '';
   };
 
-  config.settings.lang_packages = {
-    python = lib.mkDefault (with pkgs.python3Packages; [
+  config.settings.langPackageDefaults = {
+    python = with pkgs.python3Packages; [
       duckdb
       polars
-    ]);
-    r = lib.mkDefault (
-      (with pkgs.rpkgs.rPackages; [
-        arrow
-        broom
-        data_table
-        janitor
-        styler
-        # vscDebugger is not on CRAN/Bioconductor, so it is not available in
-        # pkgs.rpkgs.rPackages. Install it manually in your R library if you
-        # want to use the nvim-dap R adapter (see plugin/26_dap.lua).
-        # vscDebugger
-        lintr
-      ])
-    );
-    julia = lib.mkDefault [
+    ];
+    r = with pkgs.rpkgs.rPackages; [
+      arrow
+      broom
+      data_table
+      janitor
+      styler
+      # vscDebugger is not on CRAN/Bioconductor, so it is not available in
+      # pkgs.rpkgs.rPackages. Install it manually in your R library if you
+      # want to use the nvim-dap R adapter (see plugin/26_dap.lua).
+      # vscDebugger
+      lintr
+    ];
+    julia = [
       "DataFramesMeta"
       "QuackIO"
     ];