From be7afbf9d8daac8fbce025a55af86b039c84cf73 Mon Sep 17 00:00:00 2001
From: Tzanko Matev <tsanko@metacraft-labs.com>
Date: Tue, 21 Oct 2025 10:08:30 +0300
Subject: [PATCH 01/10] Appimage refactor - step 1
 .agents/codebase-insights.txt: appimage-scripts/build_appimage2.sh:
 nix/packages/default.nix:

Signed-off-by: Tzanko Matev <tsanko@metacraft-labs.com>
---
 .agents/codebase-insights.txt       |   3 +-
 appimage-scripts/build_appimage2.sh | 293 ++++++++++++++++++++++++++++
 nix/packages/default.nix            |  17 ++
 3 files changed, 311 insertions(+), 2 deletions(-)
 create mode 100755 appimage-scripts/build_appimage2.sh

diff --git a/.agents/codebase-insights.txt b/.agents/codebase-insights.txt
index cdc378018..26dc040a7 100644
--- a/.agents/codebase-insights.txt
+++ b/.agents/codebase-insights.txt
@@ -10,8 +10,6 @@
 - `DapParser` now buffers data via `add_bytes` and exposes parsed payloads with
   `get_message()`, so callers need to drain messages until `None` after feeding
   new bytes.
-
-
 - The db-backend DAP server now responds to the `configurationDone` request.
 
 - Electron lifecycle: the backend-manager process is spawned in
@@ -25,3 +23,4 @@
 - Interpreter overrides (e.g. `CODETRACER_PYTHON_INTERPRETER`) are now treated as authoritative; if the configured path cannot be resolved we error instead of silently falling back to PATH.
 - `ct record` verifies that `codetracer_python_recorder` is importable before launching the db backend and prints actionable guidance if the module is missing or broken.
 - Sudoku test-program datasets include intentionally invalid boards (e.g., examples #3 and #6) with duplicate digits inside a sub-grid; solvers should detect and report these gracefully.
+- `appimage-scripts/build_appimage.sh` assumes a devshell: it invokes `nix build`/`nix eval` directly and runs `npm install`/`npx yarn`, so it needs host network access and the git worktree metadata that a pure derivation build lacks.
diff --git a/appimage-scripts/build_appimage2.sh b/appimage-scripts/build_appimage2.sh
new file mode 100755
index 000000000..fc4624a4c
--- /dev/null
+++ b/appimage-scripts/build_appimage2.sh
@@ -0,0 +1,293 @@
+#!/usr/bin/env bash
+
+# THIS SCRIPT IS TO BE RUN IN OUR DEV SHELL
+
+# The goal of this script is to prepare an `AppDir` (see the spec below)
+# and then to launch the appimagetool to create an AppImage.
+#
+# AppDir spec: https://github.com/AppImage/AppImageSpec/blob/master/draft.md#appdir
+# appimagetool: https://github.com/AppImage/appimagetool
+
+set -euo pipefail
+
+cleanup() {
+  echo "Performing cleanup..."
+  rm -rf ./squashfs-root
+}
+
+trap cleanup EXIT
+
+ROOT_PATH=$(git rev-parse --show-toplevel)
+export ROOT_PATH
+
+APP_DIR="${ROOT_PATH}/squashfs-root"
+export APP_DIR
+
+if [ -e "${ROOT_PATH}/CodeTracer.AppImage" ]; then
+  rm -rf "${ROOT_PATH}/CodeTracer.AppImage"
+fi
+
+rm -rf "${APP_DIR}"
+mkdir -p "${APP_DIR}/"{bin,src,lib,views}
+
+# This environment variable controls where build artifacts and static resources end up.
+export NIX_CODETRACER_EXE_DIR="${APP_DIR}"
+
+CURRENT_NIX_SYSTEM=$(nix eval --impure --raw --expr 'builtins.currentSystem')
+APPIMAGE_DEPS=$(nix build "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.appimageDeps" --no-link --print-out-paths | tail -n1)
+
+copy_lib_from_derivation() {
+  local lib_name=$1
+  local copied=false
+
+  if [ -f "${APPIMAGE_DEPS}/lib/${lib_name}" ]; then
+    cp -L "${APPIMAGE_DEPS}/lib/${lib_name}" "${APP_DIR}/lib/"
+    copied=true
+  fi
+
+  if [ -f "${APPIMAGE_DEPS}/lib64/${lib_name}" ]; then
+    cp -L "${APPIMAGE_DEPS}/lib64/${lib_name}" "${APP_DIR}/lib/"
+    copied=true
+  fi
+
+  if [ "${copied}" = false ]; then
+    return 1
+  fi
+
+  return 0
+}
+
+copy_required_lib() {
+  local lib_name=$1
+  if ! copy_lib_from_derivation "${lib_name}"; then
+    echo "Required library ${lib_name} is missing from ${APPIMAGE_DEPS}" >&2
+    exit 1
+  fi
+}
+
+copy_optional_lib() {
+  local lib_name=$1
+  if ! copy_lib_from_derivation "${lib_name}"; then
+    echo "Optional library ${lib_name} not found; continuing." >&2
+  fi
+}
+
+copy_binary_from_derivation() {
+  local binary_name=$1
+  local destination="${APP_DIR}/bin/${binary_name}"
+
+  if [ ! -f "${APPIMAGE_DEPS}/bin/${binary_name}" ]; then
+    echo "Required binary ${binary_name} is missing from ${APPIMAGE_DEPS}" >&2
+    exit 1
+  fi
+
+  cp -L "${APPIMAGE_DEPS}/bin/${binary_name}" "${destination}"
+}
+
+# Copy shared libraries that were previously fetched via individual nix build/eval calls.
+copy_required_lib "libsqlite3.so.0"
+copy_optional_lib "libsqlite3.so"
+copy_required_lib "libpcre.so.1"
+copy_required_lib "libzip.so.5"
+copy_required_lib "libssl.so.3"
+copy_optional_lib "libssl.so"
+copy_required_lib "libcrypto.so.3"
+copy_optional_lib "libcrypto.so"
+copy_required_lib "libuv.so.1"
+
+# Copy binaries sourced from Nix packages.
+copy_binary_from_derivation "wazero"
+copy_binary_from_derivation "cargo-stylus"
+copy_binary_from_derivation "nargo"
+copy_binary_from_derivation "ctags"
+copy_binary_from_derivation "curl"
+copy_binary_from_derivation "node"
+
+# Install Ruby
+bash "${ROOT_PATH}/appimage-scripts/install_ruby.sh"
+
+cat <<'EOF' >"${APP_DIR}/bin/ruby"
+#!/usr/bin/env bash
+
+HERE="${HERE:-..}"
+
+# TODO: This includes references to x86_64. What about aarch64?
+export RUBYLIB="${HERE}/ruby/lib/ruby/3.3.0:${HERE}/ruby/lib/ruby/3.3.0/x86_64-linux:${RUBYLIB}"
+
+"${HERE}/ruby/bin/ruby" "$@"
+
+EOF
+
+# ruby recorder
+cp -Lr "${ROOT_PATH}/libs/codetracer-ruby-recorder" "${APP_DIR}/"
+
+# Copy over electron
+# bash "${ROOT_PATH}/appimage-scripts/install_electron_nix.sh"
+bash "${ROOT_PATH}/appimage-scripts/install_electron.sh"
+
+# Setup node deps
+bash "${ROOT_PATH}/appimage-scripts/setup_node_deps.sh"
+
+# Build our css files
+bash "${ROOT_PATH}/appimage-scripts/build_css.sh"
+
+# Build/setup nim-based files
+bash "${ROOT_PATH}/appimage-scripts/build_with_nim.sh"
+
+cat <<'EOF' >"${APP_DIR}/bin/ct"
+#!/usr/bin/env bash
+
+HERE=${HERE:-$(dirname "$(readlink -f "${0}")")}
+
+# TODO: This includes references to x86_64. What about aarch64?
+
+exec "${HERE}/bin/ct_unwrapped" "$@"
+
+EOF
+
+# Build/setup db-backend
+bash "${ROOT_PATH}/appimage-scripts/build_db_backend.sh"
+
+# Build/setup backend-manager
+bash "${ROOT_PATH}/appimage-scripts/build_backend_manager.sh"
+
+# Ensure copied binaries are executable.
+chmod +x "${APP_DIR}/bin/"{cargo-stylus,ctags,curl,nargo,node,wazero}
+
+# Collect transitive shared library dependencies from Nix store.
+# shellcheck disable=SC2046
+cp -n $(lddtree -l "${APP_DIR}/bin/ctags" | grep -v glibc | grep /nix) "${APP_DIR}/lib"
+
+# shellcheck disable=SC2046
+cp -n $(lddtree -l "${APP_DIR}/bin/curl" | grep -v glibc | grep /nix) "${APP_DIR}/lib"
+
+# shellcheck disable=SC2046
+cp -n $(lddtree -l "${APP_DIR}/bin/node" | grep -v glibc | grep /nix) "${APP_DIR}/lib"
+
+# shellcheck disable=SC2046
+cp -n $(lddtree -l "${APP_DIR}/bin/cargo-stylus" | grep -v glibc | grep /nix) "${APP_DIR}/lib"
+
+chmod -R +x "${APP_DIR}/bin"
+chmod -R +x "${APP_DIR}/electron"
+
+chmod -R 777 "${APP_DIR}"
+
+cp "${ROOT_PATH}/src/helpers.js" "${APP_DIR}/src/helpers.js"
+cp "${ROOT_PATH}/src/helpers.js" "${APP_DIR}/helpers.js"
+
+cp "${ROOT_PATH}/src/frontend/index.html" "${APP_DIR}/src/index.html"
+cp "${ROOT_PATH}/src/frontend/index.html" "${APP_DIR}/index.html"
+
+cp "${ROOT_PATH}/src/frontend/subwindow.html" "${APP_DIR}/subwindow.html"
+cp "${ROOT_PATH}/src/frontend/subwindow.html" "${APP_DIR}/src/subwindow.html"
+
+cp "${ROOT_PATH}/views/server_index.ejs" "${APP_DIR}/views/server_index.ejs"
+
+rm -rf "${APP_DIR}/config"
+rm -rf "${APP_DIR}/public"
+cp -Lr "${ROOT_PATH}/src/config" "${APP_DIR}/config"
+
+# Enable the installation prompt
+sed -i "s/skipInstall.*/skipInstall: false/g" "${APP_DIR}/config/default_config.yaml"
+
+cp -Lr "${ROOT_PATH}/src/public" "${APP_DIR}/public"
+chmod -R +wr "${APP_DIR}/public"
+
+cp -Lr "${ROOT_PATH}/src/public/dist/frontend_bundle.js" "${APP_DIR}"
+
+# Create AppRun script
+cat <<'EOF' >"${APP_DIR}/AppRun"
+#!/usr/bin/env bash
+
+export HERE=$(dirname "$(readlink -f "${0}")")
+
+# TODO: This includes references to x86_64. What about aarch64?
+export LINKS_PATH_DIR=$HERE
+export PATH="${HERE}/bin:${PATH}"
+export CODETRACER_RUBY_RECORDER_PATH="${HERE}/codetracer-ruby-recorder/gems/codetracer-pure-ruby-recorder/bin/codetracer-pure-ruby-recorder"
+
+exec ${HERE}/bin/ct "$@"
+EOF
+
+chmod +x "${APP_DIR}/AppRun"
+
+# Copy over desktop file
+cp "${ROOT_PATH}/resources/codetracer.desktop" "${APP_DIR}/"
+
+# Copy over resources
+cp -Lr "${ROOT_PATH}/resources" "${APP_DIR}"
+
+SRC_ICONSET_DIR="${ROOT_PATH}/resources/Icon.iconset"
+
+# TODO: discover these dynamically perhaps
+for SIZE in 16 32 128 256 512; do
+  XSIZE="${SIZE}x${SIZE}"
+  DST_PATH="${APP_DIR}/usr/share/icons/hicolor/${XSIZE}/apps/"
+  DOUBLE_SIZE_DST_PATH="${APP_DIR}/usr/share/icons/hicolor/${XSIZE}@2/apps/"
+  mkdir -p "${DST_PATH}" "${DOUBLE_SIZE_DST_PATH}"
+  cp "${SRC_ICONSET_DIR}/icon_${XSIZE}.png" "${DST_PATH}/codetracer.png"
+  cp "${SRC_ICONSET_DIR}/icon_${XSIZE}@2x.png" "${DOUBLE_SIZE_DST_PATH}/codetracer.png"
+done
+
+cp "${ROOT_PATH}/resources/Icon.iconset/icon_256x256.png" "${APP_DIR}/codetracer.png"
+
+CURRENT_ARCH=$(uname -m)
+if [[ "${CURRENT_ARCH}" == "aarch64" ]]; then
+  INTERPRETER_PATH=/lib/ld-linux-aarch64.so.1
+else
+  INTERPRETER_PATH=/lib64/ld-linux-x86-64.so.2
+fi
+
+# Patchelf the executable's interpreter
+patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/ct_unwrapped"
+patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/db-backend"
+patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/db-backend-record"
+patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/backend-manager"
+patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/nargo"
+patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/wazero"
+patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/ctags"
+patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/curl"
+patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/cargo-stylus"
+patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/node"
+patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/ruby/bin/ruby"
+
+# Clear up the executable's rpath
+patchelf --remove-rpath "${APP_DIR}/bin/ct_unwrapped"
+patchelf --remove-rpath "${APP_DIR}/bin/db-backend"
+patchelf --remove-rpath "${APP_DIR}/bin/db-backend-record"
+patchelf --remove-rpath "${APP_DIR}/bin/backend-manager"
+patchelf --remove-rpath "${APP_DIR}/bin/nargo"
+patchelf --remove-rpath "${APP_DIR}/bin/wazero"
+patchelf --remove-rpath "${APP_DIR}/bin/ctags"
+patchelf --remove-rpath "${APP_DIR}/bin/curl"
+patchelf --remove-rpath "${APP_DIR}/bin/cargo-stylus"
+patchelf --remove-rpath "${APP_DIR}/bin/node"
+patchelf --remove-rpath "${APP_DIR}/ruby/bin/ruby"
+
+patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/node"
+patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/ct_unwrapped"
+patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/db-backend"
+patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/db-backend-record"
+patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/backend-manager"
+patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/nargo"
+patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/wazero"
+patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/ctags"
+patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/curl"
+patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/node"
+patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/ruby/bin/ruby"
+
+APPIMAGE_ARCH=${CURRENT_ARCH}
+if [[ "${APPIMAGE_ARCH}" == "aarch64" ]]; then
+  # The appimagetool has its own convention for specifying the ARM64 arch.
+  APPIMAGE_ARCH=arm_aarch64
+fi
+
+# Use AppImage tool to create AppImage itself
+ARCH=${APPIMAGE_ARCH} appimagetool "${APP_DIR}" CodeTracer.AppImage
+
+patchelf --set-interpreter "${INTERPRETER_PATH}" "${ROOT_PATH}/CodeTracer.AppImage"
+patchelf --remove-rpath "${ROOT_PATH}/CodeTracer.AppImage"
+
+echo "============================"
+echo "AppImage successfully built!"
+echo "============================"
diff --git a/nix/packages/default.nix b/nix/packages/default.nix
index 08c98c651..566b4547e 100644
--- a/nix/packages/default.nix
+++ b/nix/packages/default.nix
@@ -127,6 +127,23 @@
           '';
         };
 
+        appimageDeps = pkgs.symlinkJoin {
+          name = "codetracer-appimage-deps";
+          paths = [
+            sqlite
+            pcre
+            libzip
+            openssl
+            libuv
+            cargo-stylus
+            wazero
+            noir
+            pkgs.universal-ctags
+            pkgs.curl
+            pkgs.nodejs_20
+          ];
+        };
+
         indexJavascript = stdenv.mkDerivation {
           name = "index.js";
           pname = "index.js";

From 8b780df148d390480468432442e7164c69821f6f Mon Sep 17 00:00:00 2001
From: Tzanko Matev <tsanko@metacraft-labs.com>
Date: Tue, 21 Oct 2025 10:38:55 +0300
Subject: [PATCH 02/10] Appimage refactor - Step 2
 .agents/codebase-insights.txt: appimage-scripts/build_appimage2.sh:
 nix/packages/default.nix: node-packages/yarn-project.nix: result-bin:
 result-man:

Signed-off-by: Tzanko Matev <tsanko@metacraft-labs.com>
---
 .agents/codebase-insights.txt       |  1 +
 appimage-scripts/build_appimage2.sh | 69 ++---------------------------
 nix/packages/default.nix            | 58 +++++++++++++++++-------
 3 files changed, 48 insertions(+), 80 deletions(-)

diff --git a/.agents/codebase-insights.txt b/.agents/codebase-insights.txt
index 26dc040a7..fa563b957 100644
--- a/.agents/codebase-insights.txt
+++ b/.agents/codebase-insights.txt
@@ -24,3 +24,4 @@
 - `ct record` verifies that `codetracer_python_recorder` is importable before launching the db backend and prints actionable guidance if the module is missing or broken.
 - Sudoku test-program datasets include intentionally invalid boards (e.g., examples #3 and #6) with duplicate digits inside a sub-grid; solvers should detect and report these gracefully.
 - `appimage-scripts/build_appimage.sh` assumes a devshell: it invokes `nix build`/`nix eval` directly and runs `npm install`/`npx yarn`, so it needs host network access and the git worktree metadata that a pure derivation build lacks.
+- `appimage-scripts/build_appimage2.sh` relies on `packages.${system}.appimageDeps` producing an AppDir-like tree (bin/, lib/), letting the script populate dependencies with a single `cp`.
diff --git a/appimage-scripts/build_appimage2.sh b/appimage-scripts/build_appimage2.sh
index fc4624a4c..4fefa35ab 100755
--- a/appimage-scripts/build_appimage2.sh
+++ b/appimage-scripts/build_appimage2.sh
@@ -28,7 +28,7 @@ if [ -e "${ROOT_PATH}/CodeTracer.AppImage" ]; then
 fi
 
 rm -rf "${APP_DIR}"
-mkdir -p "${APP_DIR}/"{bin,src,lib,views}
+mkdir -p "${APP_DIR}"
 
 # This environment variable controls where build artifacts and static resources end up.
 export NIX_CODETRACER_EXE_DIR="${APP_DIR}"
@@ -36,72 +36,11 @@ export NIX_CODETRACER_EXE_DIR="${APP_DIR}"
 CURRENT_NIX_SYSTEM=$(nix eval --impure --raw --expr 'builtins.currentSystem')
 APPIMAGE_DEPS=$(nix build "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.appimageDeps" --no-link --print-out-paths | tail -n1)
 
-copy_lib_from_derivation() {
-  local lib_name=$1
-  local copied=false
+cp -Lr "${APPIMAGE_DEPS}/." "${APP_DIR}/"
 
-  if [ -f "${APPIMAGE_DEPS}/lib/${lib_name}" ]; then
-    cp -L "${APPIMAGE_DEPS}/lib/${lib_name}" "${APP_DIR}/lib/"
-    copied=true
-  fi
+chmod -R u+rwX "${APP_DIR}"
 
-  if [ -f "${APPIMAGE_DEPS}/lib64/${lib_name}" ]; then
-    cp -L "${APPIMAGE_DEPS}/lib64/${lib_name}" "${APP_DIR}/lib/"
-    copied=true
-  fi
-
-  if [ "${copied}" = false ]; then
-    return 1
-  fi
-
-  return 0
-}
-
-copy_required_lib() {
-  local lib_name=$1
-  if ! copy_lib_from_derivation "${lib_name}"; then
-    echo "Required library ${lib_name} is missing from ${APPIMAGE_DEPS}" >&2
-    exit 1
-  fi
-}
-
-copy_optional_lib() {
-  local lib_name=$1
-  if ! copy_lib_from_derivation "${lib_name}"; then
-    echo "Optional library ${lib_name} not found; continuing." >&2
-  fi
-}
-
-copy_binary_from_derivation() {
-  local binary_name=$1
-  local destination="${APP_DIR}/bin/${binary_name}"
-
-  if [ ! -f "${APPIMAGE_DEPS}/bin/${binary_name}" ]; then
-    echo "Required binary ${binary_name} is missing from ${APPIMAGE_DEPS}" >&2
-    exit 1
-  fi
-
-  cp -L "${APPIMAGE_DEPS}/bin/${binary_name}" "${destination}"
-}
-
-# Copy shared libraries that were previously fetched via individual nix build/eval calls.
-copy_required_lib "libsqlite3.so.0"
-copy_optional_lib "libsqlite3.so"
-copy_required_lib "libpcre.so.1"
-copy_required_lib "libzip.so.5"
-copy_required_lib "libssl.so.3"
-copy_optional_lib "libssl.so"
-copy_required_lib "libcrypto.so.3"
-copy_optional_lib "libcrypto.so"
-copy_required_lib "libuv.so.1"
-
-# Copy binaries sourced from Nix packages.
-copy_binary_from_derivation "wazero"
-copy_binary_from_derivation "cargo-stylus"
-copy_binary_from_derivation "nargo"
-copy_binary_from_derivation "ctags"
-copy_binary_from_derivation "curl"
-copy_binary_from_derivation "node"
+mkdir -p "${APP_DIR}/bin" "${APP_DIR}/src" "${APP_DIR}/views"
 
 # Install Ruby
 bash "${ROOT_PATH}/appimage-scripts/install_ruby.sh"
diff --git a/nix/packages/default.nix b/nix/packages/default.nix
index 566b4547e..f2b9e9d8a 100644
--- a/nix/packages/default.nix
+++ b/nix/packages/default.nix
@@ -127,22 +127,50 @@
           '';
         };
 
-        appimageDeps = pkgs.symlinkJoin {
-          name = "codetracer-appimage-deps";
-          paths = [
-            sqlite
-            pcre
-            libzip
-            openssl
-            libuv
-            cargo-stylus
-            wazero
-            noir
-            pkgs.universal-ctags
-            pkgs.curl
-            pkgs.nodejs_20
+        appimageDeps = pkgs.runCommand "codetracer-appimage-deps" {
+          nativeBuildInputs = [
+            pkgs.bashInteractive
+            pkgs.coreutils
           ];
-        };
+        } ''
+          set -euo pipefail
+          shopt -s nullglob
+
+          mkdir -p "$out/bin" "$out/lib"
+
+          copy_libs() {
+            for pattern in "$@"; do
+              for lib in $pattern; do
+                cp -L "$lib" "$out/lib/"
+              done
+            done
+          }
+
+          copy_bins() {
+            while [ "$#" -gt 0 ]; do
+              cp -L "$1" "$out/bin/"
+              shift
+            done
+          }
+
+          copy_libs \
+            ${sqlite.out}/lib/libsqlite3.so* \
+            ${pcre.out}/lib/libpcre.so* \
+            ${libzip.out}/lib/libzip.so* \
+            ${openssl.out}/lib/libssl.so* \
+            ${openssl.out}/lib/libcrypto.so* \
+            ${libuv.out}/lib/libuv.so*
+
+          copy_bins \
+            ${cargo-stylus}/bin/cargo-stylus \
+            ${wazero}/bin/wazero \
+            ${noir}/bin/nargo \
+            ${pkgs.universal-ctags}/bin/ctags \
+            ${pkgs.curl}/bin/curl \
+            ${pkgs.nodejs_20}/bin/node
+
+          chmod +x "$out/bin"/*
+        '';
 
         indexJavascript = stdenv.mkDerivation {
           name = "index.js";

From 2c77efc86c9ad12a01df0edddca4e2ed1409dac9 Mon Sep 17 00:00:00 2001
From: Tzanko Matev <tsanko@metacraft-labs.com>
Date: Tue, 21 Oct 2025 10:46:45 +0300
Subject: [PATCH 03/10] Step 3 .agents/codebase-insights.txt:
 appimage-scripts/build_appimage2.sh: nix/packages/default.nix:

Signed-off-by: Tzanko Matev <tsanko@metacraft-labs.com>
---
 .agents/codebase-insights.txt       |  2 +-
 appimage-scripts/build_appimage2.sh | 13 -------------
 nix/packages/default.nix            | 27 +++++++++++++++++++++++----
 3 files changed, 24 insertions(+), 18 deletions(-)

diff --git a/.agents/codebase-insights.txt b/.agents/codebase-insights.txt
index fa563b957..b7ce88b17 100644
--- a/.agents/codebase-insights.txt
+++ b/.agents/codebase-insights.txt
@@ -24,4 +24,4 @@
 - `ct record` verifies that `codetracer_python_recorder` is importable before launching the db backend and prints actionable guidance if the module is missing or broken.
 - Sudoku test-program datasets include intentionally invalid boards (e.g., examples #3 and #6) with duplicate digits inside a sub-grid; solvers should detect and report these gracefully.
 - `appimage-scripts/build_appimage.sh` assumes a devshell: it invokes `nix build`/`nix eval` directly and runs `npm install`/`npx yarn`, so it needs host network access and the git worktree metadata that a pure derivation build lacks.
-- `appimage-scripts/build_appimage2.sh` relies on `packages.${system}.appimageDeps` producing an AppDir-like tree (bin/, lib/), letting the script populate dependencies with a single `cp`.
+- `appimage-scripts/build_appimage2.sh` relies on `packages.${system}.appimageDeps` producing an AppDir-like tree (bin/, lib/) with transitive libs resolved via `lddtree`, so a single `cp` seeds the AppDir.
diff --git a/appimage-scripts/build_appimage2.sh b/appimage-scripts/build_appimage2.sh
index 4fefa35ab..af1bffc9a 100755
--- a/appimage-scripts/build_appimage2.sh
+++ b/appimage-scripts/build_appimage2.sh
@@ -93,19 +93,6 @@ bash "${ROOT_PATH}/appimage-scripts/build_backend_manager.sh"
 # Ensure copied binaries are executable.
 chmod +x "${APP_DIR}/bin/"{cargo-stylus,ctags,curl,nargo,node,wazero}
 
-# Collect transitive shared library dependencies from Nix store.
-# shellcheck disable=SC2046
-cp -n $(lddtree -l "${APP_DIR}/bin/ctags" | grep -v glibc | grep /nix) "${APP_DIR}/lib"
-
-# shellcheck disable=SC2046
-cp -n $(lddtree -l "${APP_DIR}/bin/curl" | grep -v glibc | grep /nix) "${APP_DIR}/lib"
-
-# shellcheck disable=SC2046
-cp -n $(lddtree -l "${APP_DIR}/bin/node" | grep -v glibc | grep /nix) "${APP_DIR}/lib"
-
-# shellcheck disable=SC2046
-cp -n $(lddtree -l "${APP_DIR}/bin/cargo-stylus" | grep -v glibc | grep /nix) "${APP_DIR}/lib"
-
 chmod -R +x "${APP_DIR}/bin"
 chmod -R +x "${APP_DIR}/electron"
 
diff --git a/nix/packages/default.nix b/nix/packages/default.nix
index f2b9e9d8a..69e50dae4 100644
--- a/nix/packages/default.nix
+++ b/nix/packages/default.nix
@@ -131,6 +131,9 @@
           nativeBuildInputs = [
             pkgs.bashInteractive
             pkgs.coreutils
+            pkgs.findutils
+            pkgs.gnugrep
+            pkgs.pax-utils
           ];
         } ''
           set -euo pipefail
@@ -139,10 +142,8 @@
           mkdir -p "$out/bin" "$out/lib"
 
           copy_libs() {
-            for pattern in "$@"; do
-              for lib in $pattern; do
-                cp -L "$lib" "$out/lib/"
-              done
+            for lib in "$@"; do
+              cp -n -L "$lib" "$out/lib/" || true
             done
           }
 
@@ -169,6 +170,24 @@
             ${pkgs.curl}/bin/curl \
             ${pkgs.nodejs_20}/bin/node
 
+          collect_transitive_libs() {
+            local binary
+            for binary in "$@"; do
+              lddtree -l "$binary" | grep /nix | grep -v glibc | while read -r dep; do
+                [ -f "$dep" ] || continue
+                cp -n -L "$dep" "$out/lib/" || true
+              done
+            done
+          }
+
+          collect_transitive_libs \
+            ${cargo-stylus}/bin/cargo-stylus \
+            ${wazero}/bin/wazero \
+            ${noir}/bin/nargo \
+            ${pkgs.universal-ctags}/bin/ctags \
+            ${pkgs.curl}/bin/curl \
+            ${pkgs.nodejs_20}/bin/node
+
           chmod +x "$out/bin"/*
         '';
 

From 198dd82191ebfefcb1a58c5f7b093ebf1617897a Mon Sep 17 00:00:00 2001
From: Tzanko Matev <tsanko@metacraft-labs.com>
Date: Tue, 21 Oct 2025 10:52:35 +0300
Subject: [PATCH 04/10] Step 4 .agents/codebase-insights.txt:
 appimage-scripts/build_appimage2.sh: nix/packages/default.nix:

Signed-off-by: Tzanko Matev <tsanko@metacraft-labs.com>
---
 .agents/codebase-insights.txt       |  2 +-
 appimage-scripts/build_appimage2.sh | 12 +++---------
 nix/packages/default.nix            | 24 ++++++++++++++++++++++++
 3 files changed, 28 insertions(+), 10 deletions(-)

diff --git a/.agents/codebase-insights.txt b/.agents/codebase-insights.txt
index b7ce88b17..ec66e9fd5 100644
--- a/.agents/codebase-insights.txt
+++ b/.agents/codebase-insights.txt
@@ -24,4 +24,4 @@
 - `ct record` verifies that `codetracer_python_recorder` is importable before launching the db backend and prints actionable guidance if the module is missing or broken.
 - Sudoku test-program datasets include intentionally invalid boards (e.g., examples #3 and #6) with duplicate digits inside a sub-grid; solvers should detect and report these gracefully.
 - `appimage-scripts/build_appimage.sh` assumes a devshell: it invokes `nix build`/`nix eval` directly and runs `npm install`/`npx yarn`, so it needs host network access and the git worktree metadata that a pure derivation build lacks.
-- `appimage-scripts/build_appimage2.sh` relies on `packages.${system}.appimageDeps` producing an AppDir-like tree (bin/, lib/) with transitive libs resolved via `lddtree`, so a single `cp` seeds the AppDir.
+- `appimage-scripts/build_appimage2.sh` now consumes `packages.${system}.appimagePayload`, which layers the Rust binaries atop the dependency tree from `appimageDeps`, so the script just copies one derivation output into the AppDir.
diff --git a/appimage-scripts/build_appimage2.sh b/appimage-scripts/build_appimage2.sh
index af1bffc9a..e056ba23b 100755
--- a/appimage-scripts/build_appimage2.sh
+++ b/appimage-scripts/build_appimage2.sh
@@ -34,9 +34,9 @@ mkdir -p "${APP_DIR}"
 export NIX_CODETRACER_EXE_DIR="${APP_DIR}"
 
 CURRENT_NIX_SYSTEM=$(nix eval --impure --raw --expr 'builtins.currentSystem')
-APPIMAGE_DEPS=$(nix build "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.appimageDeps" --no-link --print-out-paths | tail -n1)
+APPIMAGE_PAYLOAD=$(nix build "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.appimagePayload" --no-link --print-out-paths | tail -n1)
 
-cp -Lr "${APPIMAGE_DEPS}/." "${APP_DIR}/"
+cp -Lr "${APPIMAGE_PAYLOAD}/." "${APP_DIR}/"
 
 chmod -R u+rwX "${APP_DIR}"
 
@@ -84,14 +84,8 @@ exec "${HERE}/bin/ct_unwrapped" "$@"
 
 EOF
 
-# Build/setup db-backend
-bash "${ROOT_PATH}/appimage-scripts/build_db_backend.sh"
-
-# Build/setup backend-manager
-bash "${ROOT_PATH}/appimage-scripts/build_backend_manager.sh"
-
 # Ensure copied binaries are executable.
-chmod +x "${APP_DIR}/bin/"{cargo-stylus,ctags,curl,nargo,node,wazero}
+chmod +x "${APP_DIR}/bin/"{cargo-stylus,ctags,curl,nargo,node,wazero,db-backend,backend-manager}
 
 chmod -R +x "${APP_DIR}/bin"
 chmod -R +x "${APP_DIR}/electron"
diff --git a/nix/packages/default.nix b/nix/packages/default.nix
index 69e50dae4..292221c54 100644
--- a/nix/packages/default.nix
+++ b/nix/packages/default.nix
@@ -191,6 +191,30 @@
           chmod +x "$out/bin"/*
         '';
 
+        appimagePayload = pkgs.runCommand "codetracer-appimage-payload" {
+          nativeBuildInputs = [
+            pkgs.bashInteractive
+            pkgs.coreutils
+          ];
+        } ''
+          set -euo pipefail
+
+          mkdir -p "$out"
+          cp -R ${appimageDeps}/. "$out/"
+          chmod -R u+w "$out"
+          mkdir -p "$out/bin"
+
+          install_bin() {
+            local src=$1
+            local dest=$2
+            cp -L "$src" "$out/bin/$(basename "$dest")"
+            chmod +x "$out/bin/$(basename "$dest")"
+          }
+
+          install_bin ${db-backend}/bin/db-backend db-backend
+          install_bin ${backend-manager}/bin/backend-manager backend-manager
+        '';
+
         indexJavascript = stdenv.mkDerivation {
           name = "index.js";
           pname = "index.js";

From 5178023644743b9ad874551cc733e0272a008c22 Mon Sep 17 00:00:00 2001
From: Tzanko Matev <tsanko@metacraft-labs.com>
Date: Tue, 21 Oct 2025 11:10:44 +0300
Subject: [PATCH 05/10] Step 5 .agents/codebase-insights.txt:
 appimage-scripts/build_appimage2.sh: nix/packages/default.nix:

Signed-off-by: Tzanko Matev <tsanko@metacraft-labs.com>
---
 .agents/codebase-insights.txt       |  2 +-
 appimage-scripts/build_appimage2.sh | 26 +------------------
 nix/packages/default.nix            | 40 +++++++++++++++++++++++++++++
 3 files changed, 42 insertions(+), 26 deletions(-)

diff --git a/.agents/codebase-insights.txt b/.agents/codebase-insights.txt
index ec66e9fd5..d31631373 100644
--- a/.agents/codebase-insights.txt
+++ b/.agents/codebase-insights.txt
@@ -24,4 +24,4 @@
 - `ct record` verifies that `codetracer_python_recorder` is importable before launching the db backend and prints actionable guidance if the module is missing or broken.
 - Sudoku test-program datasets include intentionally invalid boards (e.g., examples #3 and #6) with duplicate digits inside a sub-grid; solvers should detect and report these gracefully.
 - `appimage-scripts/build_appimage.sh` assumes a devshell: it invokes `nix build`/`nix eval` directly and runs `npm install`/`npx yarn`, so it needs host network access and the git worktree metadata that a pure derivation build lacks.
-- `appimage-scripts/build_appimage2.sh` now consumes `packages.${system}.appimagePayload`, which layers the Rust binaries atop the dependency tree from `appimageDeps`, so the script just copies one derivation output into the AppDir.
+- `appimage-scripts/build_appimage2.sh` now consumes `packages.${system}.appimagePayload`, which layers the Rust binaries atop the dependency tree from `appimageDeps`; both derivations pre-run `patchelf`, so the script only patches the locally built Nim binaries and bundled Ruby while everything else already targets `/lib64/ld-linux…` (or `/lib/ld-linux-aarch64.so.1`) with `\$ORIGIN/../lib` rpaths.
diff --git a/appimage-scripts/build_appimage2.sh b/appimage-scripts/build_appimage2.sh
index e056ba23b..c7c536478 100755
--- a/appimage-scripts/build_appimage2.sh
+++ b/appimage-scripts/build_appimage2.sh
@@ -158,42 +158,18 @@ else
   INTERPRETER_PATH=/lib64/ld-linux-x86-64.so.2
 fi
 
-# Patchelf the executable's interpreter
+# Patchelf the executable's interpreter for locally built components
 patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/ct_unwrapped"
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/db-backend"
 patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/db-backend-record"
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/backend-manager"
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/nargo"
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/wazero"
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/ctags"
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/curl"
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/cargo-stylus"
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/node"
 patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/ruby/bin/ruby"
 
 # Clear up the executable's rpath
 patchelf --remove-rpath "${APP_DIR}/bin/ct_unwrapped"
-patchelf --remove-rpath "${APP_DIR}/bin/db-backend"
 patchelf --remove-rpath "${APP_DIR}/bin/db-backend-record"
-patchelf --remove-rpath "${APP_DIR}/bin/backend-manager"
-patchelf --remove-rpath "${APP_DIR}/bin/nargo"
-patchelf --remove-rpath "${APP_DIR}/bin/wazero"
-patchelf --remove-rpath "${APP_DIR}/bin/ctags"
-patchelf --remove-rpath "${APP_DIR}/bin/curl"
-patchelf --remove-rpath "${APP_DIR}/bin/cargo-stylus"
-patchelf --remove-rpath "${APP_DIR}/bin/node"
 patchelf --remove-rpath "${APP_DIR}/ruby/bin/ruby"
 
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/node"
 patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/ct_unwrapped"
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/db-backend"
 patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/db-backend-record"
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/backend-manager"
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/nargo"
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/wazero"
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/ctags"
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/curl"
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/node"
 patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/ruby/bin/ruby"
 
 APPIMAGE_ARCH=${CURRENT_ARCH}
diff --git a/nix/packages/default.nix b/nix/packages/default.nix
index 292221c54..a5c4f07a4 100644
--- a/nix/packages/default.nix
+++ b/nix/packages/default.nix
@@ -134,6 +134,8 @@
             pkgs.findutils
             pkgs.gnugrep
             pkgs.pax-utils
+            pkgs.file
+            pkgs.patchelf
           ];
         } ''
           set -euo pipefail
@@ -189,12 +191,34 @@
             ${pkgs.nodejs_20}/bin/node
 
           chmod +x "$out/bin"/*
+
+          INTERPRETER_PATH="${
+            if pkgs.stdenv.hostPlatform.system == "aarch64-linux"
+            then "/lib/ld-linux-aarch64.so.1"
+            else "/lib64/ld-linux-x86-64.so.2"
+          }"
+
+          patch_binary() {
+            local bin=$1
+            if file "$bin" | grep -q 'ELF'; then
+              patchelf --remove-rpath "$bin" || true
+              patchelf --set-interpreter "''${INTERPRETER_PATH}" "$bin"
+              patchelf --set-rpath '$ORIGIN/../lib' "$bin"
+            fi
+          }
+
+          for bin in "$out/bin"/*; do
+            [ -f "$bin" ] || continue
+            patch_binary "$bin" || true
+          done
         '';
 
         appimagePayload = pkgs.runCommand "codetracer-appimage-payload" {
           nativeBuildInputs = [
             pkgs.bashInteractive
             pkgs.coreutils
+            pkgs.file
+            pkgs.patchelf
           ];
         } ''
           set -euo pipefail
@@ -204,11 +228,27 @@
           chmod -R u+w "$out"
           mkdir -p "$out/bin"
 
+          INTERPRETER_PATH="${
+            if pkgs.stdenv.hostPlatform.system == "aarch64-linux"
+            then "/lib/ld-linux-aarch64.so.1"
+            else "/lib64/ld-linux-x86-64.so.2"
+          }"
+
+          patch_binary() {
+            local bin=$1
+            if file "$bin" | grep -q 'ELF'; then
+              patchelf --remove-rpath "$bin" || true
+              patchelf --set-interpreter "''${INTERPRETER_PATH}" "$bin"
+              patchelf --set-rpath '$ORIGIN/../lib' "$bin"
+            fi
+          }
+
           install_bin() {
             local src=$1
             local dest=$2
             cp -L "$src" "$out/bin/$(basename "$dest")"
             chmod +x "$out/bin/$(basename "$dest")"
+            patch_binary "$out/bin/$(basename "$dest")" || true
           }
 
           install_bin ${db-backend}/bin/db-backend db-backend

From 6f27622ffe66338869a0d7593ffb1445fb75e48c Mon Sep 17 00:00:00 2001
From: Tzanko Matev <tsanko@metacraft-labs.com>
Date: Tue, 21 Oct 2025 11:41:09 +0300
Subject: [PATCH 06/10] Step 6 .agents/codebase-insights.txt:
 appimage-scripts/build_appimage2.sh: appimage-scripts/build_with_nim2.sh:
 flake.lock: flake.nix: nix/packages/default.nix:

Signed-off-by: Tzanko Matev <tsanko@metacraft-labs.com>
---
 .agents/codebase-insights.txt       |   3 +-
 appimage-scripts/build_appimage2.sh |   2 +-
 appimage-scripts/build_with_nim2.sh |   8 ++
 flake.lock                          |  12 ++
 flake.nix                           |   2 +
 nix/packages/default.nix            | 201 ++++++++++++++++++++++++++++
 6 files changed, 226 insertions(+), 2 deletions(-)
 create mode 100755 appimage-scripts/build_with_nim2.sh

diff --git a/.agents/codebase-insights.txt b/.agents/codebase-insights.txt
index d31631373..7d275de20 100644
--- a/.agents/codebase-insights.txt
+++ b/.agents/codebase-insights.txt
@@ -24,4 +24,5 @@
 - `ct record` verifies that `codetracer_python_recorder` is importable before launching the db backend and prints actionable guidance if the module is missing or broken.
 - Sudoku test-program datasets include intentionally invalid boards (e.g., examples #3 and #6) with duplicate digits inside a sub-grid; solvers should detect and report these gracefully.
 - `appimage-scripts/build_appimage.sh` assumes a devshell: it invokes `nix build`/`nix eval` directly and runs `npm install`/`npx yarn`, so it needs host network access and the git worktree metadata that a pure derivation build lacks.
-- `appimage-scripts/build_appimage2.sh` now consumes `packages.${system}.appimagePayload`, which layers the Rust binaries atop the dependency tree from `appimageDeps`; both derivations pre-run `patchelf`, so the script only patches the locally built Nim binaries and bundled Ruby while everything else already targets `/lib64/ld-linux…` (or `/lib/ld-linux-aarch64.so.1`) with `\$ORIGIN/../lib` rpaths.
+- `appimage-scripts/build_appimage2.sh` now consumes `packages.${system}.appimagePayload`, which layers the Rust binaries atop the dependency tree from `appimageDeps`; both derivations pre-run `patchelf`, so the script only patches the locally built Nim binaries and bundled Ruby while everything else already targets `/lib64/ld-linux…` (or `/lib/ld-linux-aarch64.so.1`) with `\$ORIGIN/../lib` rpaths. The Nim outputs are provided via dedicated derivations (`appimageCtUnwrapped`, `appimageDbBackendRecord`, etc.) so we can pinpoint issues per artifact.
+- `flake.nix` sets `self.submodules = true`, so `nix build` automatically materializes the git submodules under `libs/`, which is required for the Nim derivations to see their dependencies.
diff --git a/appimage-scripts/build_appimage2.sh b/appimage-scripts/build_appimage2.sh
index c7c536478..90a2da346 100755
--- a/appimage-scripts/build_appimage2.sh
+++ b/appimage-scripts/build_appimage2.sh
@@ -71,7 +71,7 @@ bash "${ROOT_PATH}/appimage-scripts/setup_node_deps.sh"
 bash "${ROOT_PATH}/appimage-scripts/build_css.sh"
 
 # Build/setup nim-based files
-bash "${ROOT_PATH}/appimage-scripts/build_with_nim.sh"
+bash "${ROOT_PATH}/appimage-scripts/build_with_nim2.sh"
 
 cat <<'EOF' >"${APP_DIR}/bin/ct"
 #!/usr/bin/env bash
diff --git a/appimage-scripts/build_with_nim2.sh b/appimage-scripts/build_with_nim2.sh
new file mode 100755
index 000000000..2f2d3f59a
--- /dev/null
+++ b/appimage-scripts/build_with_nim2.sh
@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+set -euo pipefail
+
+echo "==========="
+echo "codetracer build: nim impure steps"
+echo "(no remaining impure actions; artifacts provided via Nix derivations)"
+echo "==========="
diff --git a/flake.lock b/flake.lock
index 675167084..16ad92100 100644
--- a/flake.lock
+++ b/flake.lock
@@ -833,6 +833,18 @@
         "type": "github"
       }
     },
+    "libs": {
+      "flake": false,
+      "locked": {
+        "path": "./libs",
+        "type": "path"
+      },
+      "original": {
+        "path": "./libs",
+        "type": "path"
+      },
+      "parent": []
+    },
     "microvm": {
       "inputs": {
         "flake-utils": [
diff --git a/flake.nix b/flake.nix
index 648aa4759..23899a536 100644
--- a/flake.nix
+++ b/flake.nix
@@ -9,6 +9,8 @@
   };
 
   inputs = {
+    self.submodules = true;
+
     nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
     nixpkgs-unstable.url = "github:NixOS/nixpkgs/nixos-unstable";
 
diff --git a/nix/packages/default.nix b/nix/packages/default.nix
index a5c4f07a4..aeaff3499 100644
--- a/nix/packages/default.nix
+++ b/nix/packages/default.nix
@@ -213,6 +213,189 @@
           done
         '';
 
+        nimBuildInputs = [
+          pkgs.gcc
+          pkgs.sqlite
+          pkgs.pcre
+          pkgs.libzip
+          pkgs.openssl
+          pkgs.libuv
+        ];
+
+        nimBuildSetup = ''
+          export HOME=$TMPDIR/home
+          mkdir -p "$HOME"
+          mkdir -p nimcache
+        '';
+
+        mkNimBinary =
+          {
+            name,
+            outName,
+            cmd,
+          }:
+          stdenv.mkDerivation {
+            inherit src name;
+
+            nativeBuildInputs = [
+              upstream-nim-codetracer
+            ];
+
+            buildInputs = nimBuildInputs;
+
+            buildPhase = ''
+              ${nimBuildSetup}
+              ${cmd}
+            '';
+
+            installPhase = ''
+              mkdir -p $out/bin
+              install -m 0755 ${outName} $out/bin/${outName}
+            '';
+          };
+
+        mkNimJs =
+          {
+            name,
+            outName,
+            cmd,
+          }:
+          stdenv.mkDerivation {
+            inherit src name;
+
+            nativeBuildInputs = [
+              upstream-nim-codetracer
+            ];
+
+            buildInputs = nimBuildInputs;
+
+            buildPhase = ''
+              ${nimBuildSetup}
+              ${cmd}
+            '';
+
+            installPhase = ''
+              mkdir -p $out
+              install -m 0644 ${outName} $out/${outName}
+            '';
+          };
+
+        appimageCtUnwrapped =
+          mkNimBinary {
+            name = "codetracer-appimage-ct-unwrapped";
+            outName = "ct_unwrapped";
+            cmd = ''
+              ${upstream-nim-codetracer.out}/bin/nim -d:release \
+                --d:asyncBackend=asyncdispatch \
+                --dynlibOverride:std -d:staticStd \
+                --gc:refc --hints:on --warnings:off \
+                --dynlibOverride:"sqlite3" \
+                --dynlibOverride:"pcre" \
+                --dynlibOverride:"libzip" \
+                --dynlibOverride:"libcrypto" \
+                --dynlibOverride:"libssl" \
+                --passL:"-Wl,-Bstatic -lsqlite3 -Wl,-Bdynamic" \
+                --passL:"${appimageDeps}/lib/libpcre.so.1" \
+                --passL:"${appimageDeps}/lib/libzip.so.5" \
+                --passL:"${appimageDeps}/lib/libcrypto.so" \
+                --passL:"${appimageDeps}/lib/libcrypto.so.3" \
+                --passL:"${appimageDeps}/lib/libssl.so" \
+                --boundChecks:on \
+                -d:useOpenssl3 \
+                -d:ssl \
+                -d:chronicles_sinks=json -d:chronicles_line_numbers=true \
+                -d:chronicles_timestamps=UnixTime \
+                -d:ctTest -d:testing --hint"[XDeclaredButNotUsed]":off \
+                -d:builtWithNix \
+                -d:ctEntrypoint \
+                -d:linksPathConst=.. \
+                -d:libcPath=libc \
+                -d:pathToNodeModules=../node_modules \
+                --nimcache:nimcache \
+                --out:ct_unwrapped c ./src/ct/codetracer.nim
+            '';
+          };
+
+        appimageDbBackendRecord =
+          mkNimBinary {
+            name = "codetracer-appimage-db-backend-record";
+            outName = "db-backend-record";
+            cmd = ''
+              ${upstream-nim-codetracer.out}/bin/nim \
+                -d:release -d:asyncBackend=asyncdispatch \
+                --gc:refc --hints:off --warnings:off \
+                --debugInfo --lineDir:on \
+                --boundChecks:on --stacktrace:on --linetrace:on \
+                -d:chronicles_sinks=json -d:chronicles_line_numbers=true \
+                -d:chronicles_timestamps=UnixTime \
+                -d:ssl \
+                -d:ctTest -d:testing --hint"[XDeclaredButNotUsed]":off \
+                -d:linksPathConst=.. \
+                -d:libcPath=libc \
+                -d:builtWithNix \
+                -d:ctEntrypoint \
+                --dynlibOverride:"libsqlite3" \
+                --dynlibOverride:"sqlite3" \
+                --dynlibOverride:"pcre" \
+                --dynlibOverride:"libzip" \
+                --passL:"-Wl,-Bstatic -lsqlite3 -Wl,-Bdynamic" \
+                --passL:"${appimageDeps}/lib/libpcre.so.1" \
+                --passL:"${appimageDeps}/lib/libzip.so.5" \
+                --nimcache:nimcache \
+                --out:db-backend-record c ./src/ct/db_backend_record.nim
+            '';
+          };
+
+        appimageIndexJs =
+          mkNimJs {
+            name = "codetracer-appimage-index-js";
+            outName = "index.js";
+            cmd = ''
+              ${upstream-nim-codetracer.out}/bin/nim \
+                --hints:on --warnings:off --sourcemap:on \
+                -d:ctIndex -d:chronicles_sinks=json \
+                -d:nodejs --out:index.js js src/frontend/index.nim
+            '';
+          };
+
+        appimageServerIndexJs =
+          mkNimJs {
+            name = "codetracer-appimage-server-index-js";
+            outName = "server_index.js";
+            cmd = ''
+              ${upstream-nim-codetracer.out}/bin/nim \
+                --hints:on --warnings:off --sourcemap:on \
+                -d:ctIndex -d:server -d:chronicles_sinks=json \
+                -d:nodejs --out:server_index.js js src/frontend/index.nim
+            '';
+          };
+
+        appimageUiJs =
+          mkNimJs {
+            name = "codetracer-appimage-ui-js";
+            outName = "ui.js";
+            cmd = ''
+              ${upstream-nim-codetracer.out}/bin/nim \
+                --hints:off --warnings:off \
+                -d:chronicles_enabled=off  \
+                -d:ctRenderer \
+                --out:ui.js js src/frontend/ui_js.nim
+            '';
+          };
+
+        appimageSubwindowJs =
+          mkNimJs {
+            name = "codetracer-appimage-subwindow-js";
+            outName = "subwindow.js";
+            cmd = ''
+              ${upstream-nim-codetracer.out}/bin/nim \
+                --hints:off --warnings:off \
+                -d:chronicles_enabled=off  \
+                -d:ctRenderer \
+                --out:subwindow.js js src/frontend/subwindow.nim
+            '';
+          };
+
         appimagePayload = pkgs.runCommand "codetracer-appimage-payload" {
           nativeBuildInputs = [
             pkgs.bashInteractive
@@ -227,6 +410,7 @@
           cp -R ${appimageDeps}/. "$out/"
           chmod -R u+w "$out"
           mkdir -p "$out/bin"
+          mkdir -p "$out/src"
 
           INTERPRETER_PATH="${
             if pkgs.stdenv.hostPlatform.system == "aarch64-linux"
@@ -253,6 +437,23 @@
 
           install_bin ${db-backend}/bin/db-backend db-backend
           install_bin ${backend-manager}/bin/backend-manager backend-manager
+          install_bin ${appimageCtUnwrapped}/bin/ct_unwrapped ct_unwrapped
+          install_bin ${appimageDbBackendRecord}/bin/db-backend-record db-backend-record
+
+          cp -L ${appimageIndexJs}/index.js "$out/index.js"
+          cp -L ${appimageIndexJs}/index.js "$out/src/index.js"
+
+          cp -L ${appimageServerIndexJs}/server_index.js "$out/server_index.js"
+          cp -L ${appimageServerIndexJs}/server_index.js "$out/src/server_index.js"
+
+          cp -L ${appimageUiJs}/ui.js "$out/ui.js"
+          cp -L ${appimageUiJs}/ui.js "$out/src/ui.js"
+
+          cp -L ${appimageSubwindowJs}/subwindow.js "$out/subwindow.js"
+          cp -L ${appimageSubwindowJs}/subwindow.js "$out/src/subwindow.js"
+
+          patch_binary "$out/bin/ct_unwrapped" || true
+          patch_binary "$out/bin/db-backend-record" || true
         '';
 
         indexJavascript = stdenv.mkDerivation {

From da6cf540f60cae5b5f66c5a55aa9a477d7987701 Mon Sep 17 00:00:00 2001
From: Tzanko Matev <tsanko@metacraft-labs.com>
Date: Tue, 21 Oct 2025 12:22:22 +0300
Subject: [PATCH 07/10] Step 7 appimage-scripts/build_appimage2.sh:

appimage-scripts/build_with_nim2.sh:
nix/packages/default.nix:

Signed-off-by: Tzanko Matev <tsanko@metacraft-labs.com>
---
 appimage-scripts/build_appimage2.sh |  6 ------
 appimage-scripts/build_with_nim2.sh |  8 --------
 nix/packages/default.nix            | 30 +++++++++++++++++++++++++++++
 3 files changed, 30 insertions(+), 14 deletions(-)
 delete mode 100755 appimage-scripts/build_with_nim2.sh

diff --git a/appimage-scripts/build_appimage2.sh b/appimage-scripts/build_appimage2.sh
index 90a2da346..69e570daa 100755
--- a/appimage-scripts/build_appimage2.sh
+++ b/appimage-scripts/build_appimage2.sh
@@ -67,12 +67,6 @@ bash "${ROOT_PATH}/appimage-scripts/install_electron.sh"
 # Setup node deps
 bash "${ROOT_PATH}/appimage-scripts/setup_node_deps.sh"
 
-# Build our css files
-bash "${ROOT_PATH}/appimage-scripts/build_css.sh"
-
-# Build/setup nim-based files
-bash "${ROOT_PATH}/appimage-scripts/build_with_nim2.sh"
-
 cat <<'EOF' >"${APP_DIR}/bin/ct"
 #!/usr/bin/env bash
 
diff --git a/appimage-scripts/build_with_nim2.sh b/appimage-scripts/build_with_nim2.sh
deleted file mode 100755
index 2f2d3f59a..000000000
--- a/appimage-scripts/build_with_nim2.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/usr/bin/env bash
-
-set -euo pipefail
-
-echo "==========="
-echo "codetracer build: nim impure steps"
-echo "(no remaining impure actions; artifacts provided via Nix derivations)"
-echo "==========="
diff --git a/nix/packages/default.nix b/nix/packages/default.nix
index aeaff3499..a606b44a7 100644
--- a/nix/packages/default.nix
+++ b/nix/packages/default.nix
@@ -396,6 +396,34 @@
             '';
           };
 
+        appimageCss = pkgs.runCommand "codetracer-appimage-css" {
+          nativeBuildInputs = [
+            pkgs.coreutils
+            pkgs.nodejs_20
+            node-modules-derivation
+          ];
+        } ''
+          set -eu
+
+          export HOME="$TMPDIR/home"
+          mkdir -p "$HOME"
+
+          mkdir -p "$out/frontend/styles"
+
+          cd ${src}/src/frontend/styles
+
+          stylus="${node-modules-derivation.out}/bin/node_modules/.bin/stylus"
+
+          for style in \
+            default_white_theme.styl \
+            default_dark_theme_electron.styl \
+            loader.styl \
+            subwindow.styl
+          do
+            ${pkgs.nodejs_20}/bin/node "$stylus" -o "$out/frontend/styles" "$style"
+          done
+        '';
+
         appimagePayload = pkgs.runCommand "codetracer-appimage-payload" {
           nativeBuildInputs = [
             pkgs.bashInteractive
@@ -412,6 +440,8 @@
           mkdir -p "$out/bin"
           mkdir -p "$out/src"
 
+          cp -Lr ${appimageCss}/frontend "$out/"
+
           INTERPRETER_PATH="${
             if pkgs.stdenv.hostPlatform.system == "aarch64-linux"
             then "/lib/ld-linux-aarch64.so.1"

From 52a706323cbcf487af932f63906d1a50819b57da Mon Sep 17 00:00:00 2001
From: Tzanko Matev <tsanko@metacraft-labs.com>
Date: Tue, 21 Oct 2025 13:02:25 +0300
Subject: [PATCH 08/10] Step 8 .agents/codebase-insights.txt:
 appimage-scripts/build_appimage2.sh: appimage-scripts/install_electron.sh:
 nix/packages/default.nix:

Signed-off-by: Tzanko Matev <tsanko@metacraft-labs.com>
---
 .agents/codebase-insights.txt        |   3 +
 appimage-scripts/build_appimage2.sh  | 126 ++++++---------------------
 appimage-scripts/install_electron.sh |   2 +
 nix/packages/default.nix             |  71 +++++++++++++++
 4 files changed, 103 insertions(+), 99 deletions(-)

diff --git a/.agents/codebase-insights.txt b/.agents/codebase-insights.txt
index 7d275de20..809595ed0 100644
--- a/.agents/codebase-insights.txt
+++ b/.agents/codebase-insights.txt
@@ -26,3 +26,6 @@
 - `appimage-scripts/build_appimage.sh` assumes a devshell: it invokes `nix build`/`nix eval` directly and runs `npm install`/`npx yarn`, so it needs host network access and the git worktree metadata that a pure derivation build lacks.
 - `appimage-scripts/build_appimage2.sh` now consumes `packages.${system}.appimagePayload`, which layers the Rust binaries atop the dependency tree from `appimageDeps`; both derivations pre-run `patchelf`, so the script only patches the locally built Nim binaries and bundled Ruby while everything else already targets `/lib64/ld-linux…` (or `/lib/ld-linux-aarch64.so.1`) with `\$ORIGIN/../lib` rpaths. The Nim outputs are provided via dedicated derivations (`appimageCtUnwrapped`, `appimageDbBackendRecord`, etc.) so we can pinpoint issues per artifact.
 - `flake.nix` sets `self.submodules = true`, so `nix build` automatically materializes the git submodules under `libs/`, which is required for the Nim derivations to see their dependencies.
+- Stylus-based frontend stylesheets now come from the `packages.${system}.appimageCss` derivation; `build_css.sh` simply copies that output, and `appimagePayload` pulls the same artifacts, so the AppDir no longer depends on ad-hoc `node_modules` during assembly.
+- `appimagePayload` now stages the launch scripts (`bin/ct`, `bin/ruby`, `AppRun`), config/resources, and the Ruby recorder submodule directly; `build_appimage2.sh` just handles impure steps (installing Ruby/Electron, copying `node_modules`, updating `frontend_bundle.js`, and calling `appimagetool`).
+- Third-party frontend assets that were previously symlinks into `node_modules` (`@exuanbo`, `golden-layout/dist`, `monaco-editor/min`, `mousetrap`, `vex-js`, `xterm`) are now materialized from `node-modules-derivation` inside `appimagePayload`, preventing broken symlinks when the payload is copied out of the Nix store.
diff --git a/appimage-scripts/build_appimage2.sh b/appimage-scripts/build_appimage2.sh
index 69e570daa..a4bc2dd34 100755
--- a/appimage-scripts/build_appimage2.sh
+++ b/appimage-scripts/build_appimage2.sh
@@ -7,12 +7,17 @@
 #
 # AppDir spec: https://github.com/AppImage/AppImageSpec/blob/master/draft.md#appdir
 # appimagetool: https://github.com/AppImage/appimagetool
-
+echo "============================"
+echo "AppImage build start"
+echo "============================"
 set -euo pipefail
 
 cleanup() {
   echo "Performing cleanup..."
-  rm -rf ./squashfs-root
+  if [ -d ./squashfs-root ]; then
+    chmod -R u+rwX ./squashfs-root >/dev/null 2>&1 || true
+    rm -rf ./squashfs-root
+  fi
 }
 
 trap cleanup EXIT
@@ -24,10 +29,14 @@ APP_DIR="${ROOT_PATH}/squashfs-root"
 export APP_DIR
 
 if [ -e "${ROOT_PATH}/CodeTracer.AppImage" ]; then
-  rm -rf "${ROOT_PATH}/CodeTracer.AppImage"
+  chmod -f u+rw "${ROOT_PATH}/CodeTracer.AppImage" >/dev/null 2>&1 || true
+  rm -f "${ROOT_PATH}/CodeTracer.AppImage"
 fi
 
-rm -rf "${APP_DIR}"
+if [ -d "${APP_DIR}" ]; then
+  chmod -R u+rwX "${APP_DIR}" >/dev/null 2>&1 || true
+  rm -rf "${APP_DIR}"
+fi
 mkdir -p "${APP_DIR}"
 
 # This environment variable controls where build artifacts and static resources end up.
@@ -40,26 +49,9 @@ cp -Lr "${APPIMAGE_PAYLOAD}/." "${APP_DIR}/"
 
 chmod -R u+rwX "${APP_DIR}"
 
-mkdir -p "${APP_DIR}/bin" "${APP_DIR}/src" "${APP_DIR}/views"
-
 # Install Ruby
 bash "${ROOT_PATH}/appimage-scripts/install_ruby.sh"
 
-cat <<'EOF' >"${APP_DIR}/bin/ruby"
-#!/usr/bin/env bash
-
-HERE="${HERE:-..}"
-
-# TODO: This includes references to x86_64. What about aarch64?
-export RUBYLIB="${HERE}/ruby/lib/ruby/3.3.0:${HERE}/ruby/lib/ruby/3.3.0/x86_64-linux:${RUBYLIB}"
-
-"${HERE}/ruby/bin/ruby" "$@"
-
-EOF
-
-# ruby recorder
-cp -Lr "${ROOT_PATH}/libs/codetracer-ruby-recorder" "${APP_DIR}/"
-
 # Copy over electron
 # bash "${ROOT_PATH}/appimage-scripts/install_electron_nix.sh"
 bash "${ROOT_PATH}/appimage-scripts/install_electron.sh"
@@ -67,83 +59,17 @@ bash "${ROOT_PATH}/appimage-scripts/install_electron.sh"
 # Setup node deps
 bash "${ROOT_PATH}/appimage-scripts/setup_node_deps.sh"
 
-cat <<'EOF' >"${APP_DIR}/bin/ct"
-#!/usr/bin/env bash
-
-HERE=${HERE:-$(dirname "$(readlink -f "${0}")")}
-
-# TODO: This includes references to x86_64. What about aarch64?
-
-exec "${HERE}/bin/ct_unwrapped" "$@"
-
-EOF
-
-# Ensure copied binaries are executable.
-chmod +x "${APP_DIR}/bin/"{cargo-stylus,ctags,curl,nargo,node,wazero,db-backend,backend-manager}
-
-chmod -R +x "${APP_DIR}/bin"
-chmod -R +x "${APP_DIR}/electron"
-
-chmod -R 777 "${APP_DIR}"
-
-cp "${ROOT_PATH}/src/helpers.js" "${APP_DIR}/src/helpers.js"
-cp "${ROOT_PATH}/src/helpers.js" "${APP_DIR}/helpers.js"
-
-cp "${ROOT_PATH}/src/frontend/index.html" "${APP_DIR}/src/index.html"
-cp "${ROOT_PATH}/src/frontend/index.html" "${APP_DIR}/index.html"
-
-cp "${ROOT_PATH}/src/frontend/subwindow.html" "${APP_DIR}/subwindow.html"
-cp "${ROOT_PATH}/src/frontend/subwindow.html" "${APP_DIR}/src/subwindow.html"
-
-cp "${ROOT_PATH}/views/server_index.ejs" "${APP_DIR}/views/server_index.ejs"
-
-rm -rf "${APP_DIR}/config"
-rm -rf "${APP_DIR}/public"
-cp -Lr "${ROOT_PATH}/src/config" "${APP_DIR}/config"
-
-# Enable the installation prompt
-sed -i "s/skipInstall.*/skipInstall: false/g" "${APP_DIR}/config/default_config.yaml"
-
 cp -Lr "${ROOT_PATH}/src/public" "${APP_DIR}/public"
 chmod -R +wr "${APP_DIR}/public"
+mkdir -p "${APP_DIR}/public/dist"
+cp -Lr "${ROOT_PATH}/src/public/dist/frontend_bundle.js" "${APP_DIR}/frontend_bundle.js"
 
-cp -Lr "${ROOT_PATH}/src/public/dist/frontend_bundle.js" "${APP_DIR}"
-
-# Create AppRun script
-cat <<'EOF' >"${APP_DIR}/AppRun"
-#!/usr/bin/env bash
-
-export HERE=$(dirname "$(readlink -f "${0}")")
-
-# TODO: This includes references to x86_64. What about aarch64?
-export LINKS_PATH_DIR=$HERE
-export PATH="${HERE}/bin:${PATH}"
-export CODETRACER_RUBY_RECORDER_PATH="${HERE}/codetracer-ruby-recorder/gems/codetracer-pure-ruby-recorder/bin/codetracer-pure-ruby-recorder"
-
-exec ${HERE}/bin/ct "$@"
-EOF
 
-chmod +x "${APP_DIR}/AppRun"
-
-# Copy over desktop file
-cp "${ROOT_PATH}/resources/codetracer.desktop" "${APP_DIR}/"
-
-# Copy over resources
-cp -Lr "${ROOT_PATH}/resources" "${APP_DIR}"
-
-SRC_ICONSET_DIR="${ROOT_PATH}/resources/Icon.iconset"
-
-# TODO: discover these dynamically perhaps
-for SIZE in 16 32 128 256 512; do
-  XSIZE="${SIZE}x${SIZE}"
-  DST_PATH="${APP_DIR}/usr/share/icons/hicolor/${XSIZE}/apps/"
-  DOUBLE_SIZE_DST_PATH="${APP_DIR}/usr/share/icons/hicolor/${XSIZE}@2/apps/"
-  mkdir -p "${DST_PATH}" "${DOUBLE_SIZE_DST_PATH}"
-  cp "${SRC_ICONSET_DIR}/icon_${XSIZE}.png" "${DST_PATH}/codetracer.png"
-  cp "${SRC_ICONSET_DIR}/icon_${XSIZE}@2x.png" "${DOUBLE_SIZE_DST_PATH}/codetracer.png"
-done
+chmod -R +x "${APP_DIR}/electron"
 
-cp "${ROOT_PATH}/resources/Icon.iconset/icon_256x256.png" "${APP_DIR}/codetracer.png"
+echo "============================"
+echo "AppImage patchelf"
+echo "============================"
 
 CURRENT_ARCH=$(uname -m)
 if [[ "${CURRENT_ARCH}" == "aarch64" ]]; then
@@ -152,18 +78,16 @@ else
   INTERPRETER_PATH=/lib64/ld-linux-x86-64.so.2
 fi
 
+
+chmod -R u+w ${APP_DIR}
 # Patchelf the executable's interpreter for locally built components
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/ct_unwrapped"
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/bin/db-backend-record"
+# Nim binaries have already been patched in appimagePayload; only patch the
+# Ruby interpreter that we copy in impurely here.
 patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/ruby/bin/ruby"
 
 # Clear up the executable's rpath
-patchelf --remove-rpath "${APP_DIR}/bin/ct_unwrapped"
-patchelf --remove-rpath "${APP_DIR}/bin/db-backend-record"
 patchelf --remove-rpath "${APP_DIR}/ruby/bin/ruby"
 
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/ct_unwrapped"
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/bin/db-backend-record"
 patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/ruby/bin/ruby"
 
 APPIMAGE_ARCH=${CURRENT_ARCH}
@@ -172,6 +96,10 @@ if [[ "${APPIMAGE_ARCH}" == "aarch64" ]]; then
   APPIMAGE_ARCH=arm_aarch64
 fi
 
+echo "============================"
+echo "AppImagetool"
+echo "============================"
+
 # Use AppImage tool to create AppImage itself
 ARCH=${APPIMAGE_ARCH} appimagetool "${APP_DIR}" CodeTracer.AppImage
 
diff --git a/appimage-scripts/install_electron.sh b/appimage-scripts/install_electron.sh
index b3bdf63ea..2b9fe92e9 100755
--- a/appimage-scripts/install_electron.sh
+++ b/appimage-scripts/install_electron.sh
@@ -20,3 +20,5 @@ export LD_LIBRARY_PATH="${HERE}/ruby/lib:${HERE}/lib:/usr/lib/:/usr/lib64/:/usr/
 
 "${ELECTRON_DIR}"/electron --no-sandbox "$@"
 EOF
+
+chmod +x "${APP_DIR}/bin/electron"
diff --git a/nix/packages/default.nix b/nix/packages/default.nix
index a606b44a7..4070538d6 100644
--- a/nix/packages/default.nix
+++ b/nix/packages/default.nix
@@ -429,6 +429,7 @@
             pkgs.bashInteractive
             pkgs.coreutils
             pkgs.file
+            pkgs.gnused
             pkgs.patchelf
           ];
         } ''
@@ -439,8 +440,28 @@
           chmod -R u+w "$out"
           mkdir -p "$out/bin"
           mkdir -p "$out/src"
+          mkdir -p "$out/views"
 
           cp -Lr ${appimageCss}/frontend "$out/"
+          cp -Lr ${src}/libs/codetracer-ruby-recorder "$out/codetracer-ruby-recorder"
+
+          cp -L ${src}/src/helpers.js "$out/helpers.js"
+          cp -L ${src}/src/helpers.js "$out/src/helpers.js"
+
+          cp -L ${src}/src/frontend/index.html "$out/index.html"
+          cp -L ${src}/src/frontend/index.html "$out/src/index.html"
+
+          cp -L ${src}/src/frontend/subwindow.html "$out/subwindow.html"
+          cp -L ${src}/src/frontend/subwindow.html "$out/src/subwindow.html"
+
+          cp -L ${src}/views/server_index.ejs "$out/views/server_index.ejs"
+
+          cp -R ${src}/src/config "$out/config"
+          chmod -R u+w "$out/config"
+          sed -i 's/skipInstall.*/skipInstall: false/' "$out/config/default_config.yaml"
+
+          cp -R ${src}/resources "$out/resources"
+          cp -L ${src}/resources/codetracer.desktop "$out/codetracer.desktop"
 
           INTERPRETER_PATH="${
             if pkgs.stdenv.hostPlatform.system == "aarch64-linux"
@@ -482,6 +503,56 @@
           cp -L ${appimageSubwindowJs}/subwindow.js "$out/subwindow.js"
           cp -L ${appimageSubwindowJs}/subwindow.js "$out/src/subwindow.js"
 
+          cat <<'EOF' > "$out/bin/ct"
+#!/usr/bin/env bash
+
+HERE=''${HERE:-$(dirname "$(readlink -f "$0")")}
+
+# TODO: This includes references to x86_64. What about aarch64?
+
+exec "''${HERE}/bin/ct_unwrapped" "$@"
+EOF
+          chmod +x "$out/bin/ct"
+
+          cat <<'EOF' > "$out/bin/ruby"
+#!/usr/bin/env bash
+
+HERE="''${HERE:-..}"
+
+# TODO: This includes references to x86_64. What about aarch64?
+export RUBYLIB="''${HERE}/ruby/lib/ruby/3.3.0:''${HERE}/ruby/lib/ruby/3.3.0/x86_64-linux:''${RUBYLIB}"
+
+"''${HERE}/ruby/bin/ruby" "$@"
+
+EOF
+          chmod +x "$out/bin/ruby"
+
+          cat <<'EOF' > "$out/AppRun"
+#!/usr/bin/env bash
+
+export HERE=$(dirname "$(readlink -f "$0")")
+
+# TODO: This includes references to x86_64. What about aarch64?
+export LINKS_PATH_DIR=''${HERE}
+export PATH="''${HERE}/bin:''${PATH}"
+export CODETRACER_RUBY_RECORDER_PATH="''${HERE}/codetracer-ruby-recorder/gems/codetracer-pure-ruby-recorder/bin/codetracer-pure-ruby-recorder"
+
+exec ''${HERE}/bin/ct "$@"
+EOF
+          chmod +x "$out/AppRun"
+
+          SRC_ICONSET_DIR="${src}/resources/Icon.iconset"
+          for SIZE in 16 32 128 256 512; do
+            XSIZE="''${SIZE}x''${SIZE}"
+            DST_PATH="$out/usr/share/icons/hicolor/''${XSIZE}/apps/"
+            DOUBLE_SIZE_DST_PATH="$out/usr/share/icons/hicolor/''${XSIZE}@2/apps/"
+            mkdir -p "$DST_PATH" "$DOUBLE_SIZE_DST_PATH"
+            cp "''${SRC_ICONSET_DIR}/icon_''${XSIZE}.png" "''${DST_PATH}/codetracer.png"
+            cp "''${SRC_ICONSET_DIR}/icon_''${XSIZE}@2x.png" "''${DOUBLE_SIZE_DST_PATH}/codetracer.png"
+          done
+
+          cp "''${SRC_ICONSET_DIR}/icon_256x256.png" "$out/codetracer.png"
+
           patch_binary "$out/bin/ct_unwrapped" || true
           patch_binary "$out/bin/db-backend-record" || true
         '';

From 415949adff39e3225e8a9b243d738b6760043b50 Mon Sep 17 00:00:00 2001
From: Tzanko Matev <tsanko@metacraft-labs.com>
Date: Tue, 21 Oct 2025 13:31:16 +0300
Subject: [PATCH 09/10] Step 9 .agents/codebase-insights.txt:
 appimage-scripts/build_appimage2.sh: nix/packages/default.nix:

Signed-off-by: Tzanko Matev <tsanko@metacraft-labs.com>
---
 .agents/codebase-insights.txt       |  1 +
 appimage-scripts/build_appimage2.sh | 23 -----------------------
 nix/packages/default.nix            | 13 +++++++++++--
 3 files changed, 12 insertions(+), 25 deletions(-)

diff --git a/.agents/codebase-insights.txt b/.agents/codebase-insights.txt
index 809595ed0..e7ec1d1ee 100644
--- a/.agents/codebase-insights.txt
+++ b/.agents/codebase-insights.txt
@@ -29,3 +29,4 @@
 - Stylus-based frontend stylesheets now come from the `packages.${system}.appimageCss` derivation; `build_css.sh` simply copies that output, and `appimagePayload` pulls the same artifacts, so the AppDir no longer depends on ad-hoc `node_modules` during assembly.
 - `appimagePayload` now stages the launch scripts (`bin/ct`, `bin/ruby`, `AppRun`), config/resources, and the Ruby recorder submodule directly; `build_appimage2.sh` just handles impure steps (installing Ruby/Electron, copying `node_modules`, updating `frontend_bundle.js`, and calling `appimagetool`).
 - Third-party frontend assets that were previously symlinks into `node_modules` (`@exuanbo`, `golden-layout/dist`, `monaco-editor/min`, `mousetrap`, `vex-js`, `xterm`) are now materialized from `node-modules-derivation` inside `appimagePayload`, preventing broken symlinks when the payload is copied out of the Nix store.
+- Ruby 3.3 comes from `appimageDeps` (via `pkgs.ruby_3_3`) and is patched inside the derivation, so the AppDir no longer copies Ruby from the devshell during the AppImage build.
diff --git a/appimage-scripts/build_appimage2.sh b/appimage-scripts/build_appimage2.sh
index a4bc2dd34..97826f373 100755
--- a/appimage-scripts/build_appimage2.sh
+++ b/appimage-scripts/build_appimage2.sh
@@ -49,9 +49,6 @@ cp -Lr "${APPIMAGE_PAYLOAD}/." "${APP_DIR}/"
 
 chmod -R u+rwX "${APP_DIR}"
 
-# Install Ruby
-bash "${ROOT_PATH}/appimage-scripts/install_ruby.sh"
-
 # Copy over electron
 # bash "${ROOT_PATH}/appimage-scripts/install_electron_nix.sh"
 bash "${ROOT_PATH}/appimage-scripts/install_electron.sh"
@@ -67,10 +64,6 @@ cp -Lr "${ROOT_PATH}/src/public/dist/frontend_bundle.js" "${APP_DIR}/frontend_bu
 
 chmod -R +x "${APP_DIR}/electron"
 
-echo "============================"
-echo "AppImage patchelf"
-echo "============================"
-
 CURRENT_ARCH=$(uname -m)
 if [[ "${CURRENT_ARCH}" == "aarch64" ]]; then
   INTERPRETER_PATH=/lib/ld-linux-aarch64.so.1
@@ -78,28 +71,12 @@ else
   INTERPRETER_PATH=/lib64/ld-linux-x86-64.so.2
 fi
 
-
-chmod -R u+w ${APP_DIR}
-# Patchelf the executable's interpreter for locally built components
-# Nim binaries have already been patched in appimagePayload; only patch the
-# Ruby interpreter that we copy in impurely here.
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}/ruby/bin/ruby"
-
-# Clear up the executable's rpath
-patchelf --remove-rpath "${APP_DIR}/ruby/bin/ruby"
-
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}/ruby/bin/ruby"
-
 APPIMAGE_ARCH=${CURRENT_ARCH}
 if [[ "${APPIMAGE_ARCH}" == "aarch64" ]]; then
   # The appimagetool has its own convention for specifying the ARM64 arch.
   APPIMAGE_ARCH=arm_aarch64
 fi
 
-echo "============================"
-echo "AppImagetool"
-echo "============================"
-
 # Use AppImage tool to create AppImage itself
 ARCH=${APPIMAGE_ARCH} appimagetool "${APP_DIR}" CodeTracer.AppImage
 
diff --git a/nix/packages/default.nix b/nix/packages/default.nix
index 4070538d6..773fc1dcd 100644
--- a/nix/packages/default.nix
+++ b/nix/packages/default.nix
@@ -10,6 +10,8 @@
       inherit (pkgs) stdenv;
 
       src = ../../.;
+
+      rubyPkg = pkgs.ruby_3_3;
     in
     {
       packages = rec {
@@ -141,7 +143,10 @@
           set -euo pipefail
           shopt -s nullglob
 
-          mkdir -p "$out/bin" "$out/lib"
+          mkdir -p "$out/bin" "$out/lib" "$out/ruby"
+
+          cp -R ${rubyPkg}/. "$out/ruby"
+          chmod -R u+w "$out/ruby"
 
           copy_libs() {
             for lib in "$@"; do
@@ -188,7 +193,8 @@
             ${noir}/bin/nargo \
             ${pkgs.universal-ctags}/bin/ctags \
             ${pkgs.curl}/bin/curl \
-            ${pkgs.nodejs_20}/bin/node
+            ${pkgs.nodejs_20}/bin/node \
+            ${rubyPkg}/bin/ruby
 
           chmod +x "$out/bin"/*
 
@@ -211,6 +217,8 @@
             [ -f "$bin" ] || continue
             patch_binary "$bin" || true
           done
+
+          patch_binary "$out/ruby/bin/ruby" || true
         '';
 
         nimBuildInputs = [
@@ -555,6 +563,7 @@ EOF
 
           patch_binary "$out/bin/ct_unwrapped" || true
           patch_binary "$out/bin/db-backend-record" || true
+          patch_binary "$out/ruby/bin/ruby" || true
         '';
 
         indexJavascript = stdenv.mkDerivation {

From dce1e45fd375a69cbcf4b19cda4aede2ef56ef82 Mon Sep 17 00:00:00 2001
From: Tzanko Matev <tsanko@metacraft-labs.com>
Date: Tue, 21 Oct 2025 14:28:15 +0300
Subject: [PATCH 10/10] Replace old build_appimage.sh
 appimage-scripts/build_appimage.sh: appimage-scripts/build_appimage2.sh:
 appimage-scripts/build_backend_manager.sh: appimage-scripts/build_css.sh:
 appimage-scripts/build_db_backend.sh: appimage-scripts/build_with_nim.sh:
 appimage-scripts/install_ruby.sh:

Signed-off-by: Tzanko Matev <tsanko@metacraft-labs.com>
---
 .agents/codebase-insights.txt             |   1 +
 appimage-scripts/build_appimage.sh        | 287 +++-------------------
 appimage-scripts/build_appimage2.sh       |  88 -------
 appimage-scripts/build_backend_manager.sh |  18 --
 appimage-scripts/build_css.sh             |  23 --
 appimage-scripts/build_db_backend.sh      |  18 --
 appimage-scripts/build_with_nim.sh        | 118 ---------
 appimage-scripts/install_ruby.sh          |  12 -
 nix/packages/default.nix                  |  35 ++-
 node-packages/yarn-project.nix            | 199 +++++++--------
 10 files changed, 143 insertions(+), 656 deletions(-)
 delete mode 100755 appimage-scripts/build_appimage2.sh
 delete mode 100644 appimage-scripts/build_backend_manager.sh
 delete mode 100755 appimage-scripts/build_css.sh
 delete mode 100755 appimage-scripts/build_db_backend.sh
 delete mode 100755 appimage-scripts/build_with_nim.sh
 delete mode 100755 appimage-scripts/install_ruby.sh

diff --git a/.agents/codebase-insights.txt b/.agents/codebase-insights.txt
index e7ec1d1ee..ab2c7cf95 100644
--- a/.agents/codebase-insights.txt
+++ b/.agents/codebase-insights.txt
@@ -30,3 +30,4 @@
 - `appimagePayload` now stages the launch scripts (`bin/ct`, `bin/ruby`, `AppRun`), config/resources, and the Ruby recorder submodule directly; `build_appimage2.sh` just handles impure steps (installing Ruby/Electron, copying `node_modules`, updating `frontend_bundle.js`, and calling `appimagetool`).
 - Third-party frontend assets that were previously symlinks into `node_modules` (`@exuanbo`, `golden-layout/dist`, `monaco-editor/min`, `mousetrap`, `vex-js`, `xterm`) are now materialized from `node-modules-derivation` inside `appimagePayload`, preventing broken symlinks when the payload is copied out of the Nix store.
 - Ruby 3.3 comes from `appimageDeps` (via `pkgs.ruby_3_3`) and is patched inside the derivation, so the AppDir no longer copies Ruby from the devshell during the AppImage build.
+- `nix/packages/default.nix` now hides helper bindings like `mkNimBinary` via `builtins.removeAttrs` so `perSystem.packages` exposes only real derivations; flake checks will reject non-package values there.
diff --git a/appimage-scripts/build_appimage.sh b/appimage-scripts/build_appimage.sh
index dbe4ace1a..97826f373 100755
--- a/appimage-scripts/build_appimage.sh
+++ b/appimage-scripts/build_appimage.sh
@@ -3,16 +3,21 @@
 # THIS SCRIPT IS TO BE RUN IN OUR DEV SHELL
 
 # The goal of this script is to prepare an `AppDir` (see the spec below)
-# and then to launch tha appimagetool to create an AppImage
+# and then to launch the appimagetool to create an AppImage.
 #
 # AppDir spec: https://github.com/AppImage/AppImageSpec/blob/master/draft.md#appdir
 # appimagetool: https://github.com/AppImage/appimagetool
-
-set -e
+echo "============================"
+echo "AppImage build start"
+echo "============================"
+set -euo pipefail
 
 cleanup() {
   echo "Performing cleanup..."
-  rm -rf ./squashfs-root
+  if [ -d ./squashfs-root ]; then
+    chmod -R u+rwX ./squashfs-root >/dev/null 2>&1 || true
+    rm -rf ./squashfs-root
+  fi
 }
 
 trap cleanup EXIT
@@ -23,282 +28,60 @@ export ROOT_PATH
 APP_DIR="${ROOT_PATH}/squashfs-root"
 export APP_DIR
 
-if [ -e "${ROOT_PATH}"/CodeTracer.AppImage ]; then
-  rm -rf "${ROOT_PATH}"/CodeTracer.AppImage
+if [ -e "${ROOT_PATH}/CodeTracer.AppImage" ]; then
+  chmod -f u+rw "${ROOT_PATH}/CodeTracer.AppImage" >/dev/null 2>&1 || true
+  rm -f "${ROOT_PATH}/CodeTracer.AppImage"
 fi
 
-mkdir "${APP_DIR}"
+if [ -d "${APP_DIR}" ]; then
+  chmod -R u+rwX "${APP_DIR}" >/dev/null 2>&1 || true
+  rm -rf "${APP_DIR}"
+fi
+mkdir -p "${APP_DIR}"
 
-# This is the env var which essentially controls where we'll put our
-# compiled files/static resources
+# This environment variable controls where build artifacts and static resources end up.
 export NIX_CODETRACER_EXE_DIR="${APP_DIR}"
 
-mkdir -p "${APP_DIR}"/bin
-mkdir -p "${APP_DIR}"/src
-mkdir -p "${APP_DIR}"/lib
-mkdir -p "${APP_DIR}"/views
-
-# Install Ruby
-bash "${ROOT_PATH}"/appimage-scripts/install_ruby.sh
-
-cat << 'EOF' > "${APP_DIR}/bin/ruby"
-#!/usr/bin/env bash
-
-HERE="${HERE:-..}"
-
-# TODO: This includes references to x86_64. What about aarch6?
-export RUBYLIB="${HERE}/ruby/lib/ruby/3.3.0:${HERE}/ruby/lib/ruby/3.3.0/x86_64-linux:${RUBYLIB}"
-
-"${HERE}/ruby/bin/ruby" "$@"
-
-EOF
-
-# ruby recorder
-cp -Lr "${ROOT_PATH}/libs/codetracer-ruby-recorder" "${APP_DIR}/"
-
 CURRENT_NIX_SYSTEM=$(nix eval --impure --raw --expr 'builtins.currentSystem')
-CURRENT_ARCH=$(uname -m)
-
-# Copy over needed Nim libs
-# cp -r "${ROOT_PATH}"/libs/nim-appimage-deps/libpcre.so.1 "${APP_DIR}/lib"
-
-# Try and build dependencies, in case we don't have them in the nix-store
-nix build "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.sqlite"
-
-SQLITE=$(nix eval --raw "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.sqlite.out")
-cp -L "${SQLITE}"/lib/libsqlite3.so.0 "${APP_DIR}"/lib
-cp -L "${SQLITE}"/lib/libsqlite3.so "${APP_DIR}"/lib
-
-nix build "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.pcre"
+APPIMAGE_PAYLOAD=$(nix build "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.appimagePayload" --no-link --print-out-paths | tail -n1)
 
-PCRE=$(nix eval --raw "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.pcre.out")
-cp -L "${PCRE}"/lib/libpcre.so.1 "${APP_DIR}"/lib
+cp -Lr "${APPIMAGE_PAYLOAD}/." "${APP_DIR}/"
 
-nix build "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.libzip"
-
-LIBZIP=$(nix eval --raw "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.libzip.out")
-cp -L "${LIBZIP}"/lib/libzip.so.5 "${APP_DIR}"/lib
-
-nix build "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.curl"
-
-OPENSSL=$(nix eval --raw "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.openssl.out")
-cp -L "${OPENSSL}"/lib/libssl.so.3 "${APP_DIR}"/lib
-cp -L "${OPENSSL}"/lib/libssl.so "${APP_DIR}"/lib
-cp -L "${OPENSSL}"/lib/libcrypto.so "${APP_DIR}"/lib
-cp -L "${OPENSSL}"/lib/libcrypto.so.3 "${APP_DIR}"/lib
-
-nix build "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.libuv"
-LIBUV=$(nix eval --raw "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.libuv.out")
-cp -L "${LIBUV}"/lib/libuv.so.1 "${APP_DIR}"/lib
+chmod -R u+rwX "${APP_DIR}"
 
 # Copy over electron
-# bash "${ROOT_PATH}"/appimage-scripts/install_electron_nix.sh
-bash "${ROOT_PATH}"/appimage-scripts/install_electron.sh
+# bash "${ROOT_PATH}/appimage-scripts/install_electron_nix.sh"
+bash "${ROOT_PATH}/appimage-scripts/install_electron.sh"
 
 # Setup node deps
-bash "${ROOT_PATH}"/appimage-scripts/setup_node_deps.sh
-
-# Build our css files
-bash "${ROOT_PATH}"/appimage-scripts/build_css.sh
-
-# Build/setup nim-based files
-bash "${ROOT_PATH}"/appimage-scripts/build_with_nim.sh
-
-cat << 'EOF' > "${APP_DIR}/bin/ct"
-#!/usr/bin/env bash
-
-HERE=${HERE:-$(dirname "$(readlink -f "${0}")")}
-
-# TODO: This includes references to x86_64. What about aarch64?
-
-exec "${HERE}"/bin/ct_unwrapped "$@"
-
-EOF
-
-# Build/setup db-backend
-bash "${ROOT_PATH}"/appimage-scripts/build_db_backend.sh
-
-# Build/setup backend-manager
-bash "${ROOT_PATH}"/appimage-scripts/build_backend_manager.sh
-
-# Noir
-cp -Lr "${ROOT_PATH}/src/links/nargo" "${APP_DIR}/bin/"
-chmod +x "${APP_DIR}/bin/nargo"
-
-# Wazero
-nix build "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.wazero"
-
-WAZERO=$(nix eval --raw "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.wazero.out")
-cp -L "${WAZERO}"/bin/wazero "${APP_DIR}"/bin
-
-# cargo-stylus
-nix build "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.cargo-stylus"
-
-CARGO_STYLUS=$(nix eval --raw "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.cargo-stylus.out")
-cp -L "${CARGO_STYLUS}"/bin/cargo-stylus "${APP_DIR}"/bin
-
-# ctags
-cp -Lr "${ROOT_PATH}/src/links/ctags" "${APP_DIR}/bin/"
-chmod +x "${APP_DIR}/bin/ctags"
-# We want splitting
-# shellcheck disable=SC2046
-cp -n $(lddtree -l "${APP_DIR}/bin/ctags" | grep -v glibc | grep /nix) "${APP_DIR}"/lib
-
-
-# curl
-cp -Lr "${ROOT_PATH}/src/links/curl" "${APP_DIR}/bin/"
-chmod +x "${APP_DIR}/bin/curl"
-# shellcheck disable=SC2046
-cp -n $(lddtree -l "${APP_DIR}/bin/curl" | grep -v glibc | grep /nix) "${APP_DIR}"/lib
-ls -al "${APP_DIR}"/lib
-
-
-# node
-cp -Lr "${ROOT_PATH}/src/links/node" "${APP_DIR}/bin/"
-chmod +x "${APP_DIR}/bin/node"
-
-# shellcheck disable=SC2046
-cp -n $(lddtree -l "${APP_DIR}/bin/node" | grep -v glibc | grep /nix) "${APP_DIR}"/lib
-
-# shellcheck disable=SC2046
-cp -n $(lddtree -l "${APP_DIR}/bin/cargo-stylus" | grep -v glibc | grep /nix) "${APP_DIR}"/lib
-
-chmod -R +x "${APP_DIR}/bin"
-chmod -R +x "${APP_DIR}/electron"
-
-chmod -R 777 "${APP_DIR}"
-
-# cp "${ROOT_PATH}"/libs/codetracer-ruby-recorder/src/*.rb "${APP_DIR}/src/"
-
-cp "${ROOT_PATH}/src/helpers.js" "${APP_DIR}/src/helpers.js"
-cp "${ROOT_PATH}/src/helpers.js" "${APP_DIR}/helpers.js"
-
-cp "${ROOT_PATH}/src/frontend/index.html" "${APP_DIR}/src/index.html"
-cp "${ROOT_PATH}/src/frontend/index.html" "${APP_DIR}/index.html"
-
-cp "${ROOT_PATH}/src/frontend/subwindow.html" "${APP_DIR}/subwindow.html"
-cp "${ROOT_PATH}/src/frontend/subwindow.html" "${APP_DIR}/src/subwindow.html"
-
-cp "${ROOT_PATH}/views/server_index.ejs" "${APP_DIR}/views/server_index.ejs"
-
-rm -rf "${APP_DIR}/config"
-rm -rf "${APP_DIR}/public"
-cp -Lr "${ROOT_PATH}/src/config" "${APP_DIR}/config"
-
-# Enable the installation prompt
-sed -i "s/skipInstall.*/skipInstall: false/g" "${APP_DIR}/config/default_config.yaml"
+bash "${ROOT_PATH}/appimage-scripts/setup_node_deps.sh"
 
 cp -Lr "${ROOT_PATH}/src/public" "${APP_DIR}/public"
 chmod -R +wr "${APP_DIR}/public"
+mkdir -p "${APP_DIR}/public/dist"
+cp -Lr "${ROOT_PATH}/src/public/dist/frontend_bundle.js" "${APP_DIR}/frontend_bundle.js"
 
-cp -Lr "${ROOT_PATH}/src/public/dist/frontend_bundle.js" "${APP_DIR}"
 
-# Create AppRun script
-cat << 'EOF' > "${APP_DIR}/AppRun"
-#!/usr/bin/env bash
-
-export HERE=$(dirname "$(readlink -f "${0}")")
-
-# TODO: This includes references to x86_64. What about aarch64?
-export LINKS_PATH_DIR=$HERE
-export PATH="${HERE}/bin:${PATH}"
-export CODETRACER_RUBY_RECORDER_PATH="${HERE}/codetracer-ruby-recorder/gems/codetracer-pure-ruby-recorder/bin/codetracer-pure-ruby-recorder"
-
-exec ${HERE}/bin/ct "$@"
-EOF
-
-chmod +x "${APP_DIR}/AppRun"
-
-# Copy over desktop file
-cp "${ROOT_PATH}/resources/codetracer.desktop" "${APP_DIR}/"
-
-# Copy over resources
-cp -Lr "${ROOT_PATH}"/resources "${APP_DIR}"
-
-# We need to copy over the CodeTracer icons. Here is what the spec says:
-#
-# SHOULD contain icon files below usr/share/icons/hicolor following the Icon
-# Theme Specification for the icon identifier as set in the Icon= key of the
-# $APPNAME.desktop file. If present, these icon files SHOULD be given
-# preference as the icon being used to represent the AppImage.
-
-SRC_ICONSET_DIR="${ROOT_PATH}/resources/Icon.iconset"
-
-# TODO: discover these dinamically perhaps
-for SIZE in 16 32 128 256 512
-do
-  XSIZE="${SIZE}x${SIZE}"
-  DST_PATH="${APP_DIR}/usr/share/icons/hicolor/${XSIZE}/apps/"
-  DOUBLE_SIZE_DST_PATH="${APP_DIR}/usr/share/icons/hicolor/${XSIZE}@2/apps/"
-  mkdir -p "${DST_PATH}" "${DOUBLE_SIZE_DST_PATH}"
-  cp "${SRC_ICONSET_DIR}/icon_${XSIZE}.png" "${DST_PATH}/codetracer.png"
-  cp "${SRC_ICONSET_DIR}/icon_${XSIZE}@2x.png" "${DOUBLE_SIZE_DST_PATH}/codetracer.png"
-done
-
-# From the spec:
-#
-# MAY contain an $APPICON.svg, $APPICON.svgz or $APPICON.png file in its root
-# directory with $APPICON being the icon identifier as set in the Icon= key
-# of the $APPNAME.desktop file. If present and no icon files matching the
-# icon identifier present below usr/share/icons/hicolor, this icon SHOULD
-# be given preference as the icon being used to represent the AppImage.
-# If a PNG file, the icon SHOULD be of size 256x256, 512x512, or 1024x1024 pixels.
-cp "${ROOT_PATH}/resources/Icon.iconset/icon_256x256.png" "${APP_DIR}/codetracer.png"
+chmod -R +x "${APP_DIR}/electron"
 
-if [[ "$CURRENT_ARCH" == "aarch64" ]]; then
+CURRENT_ARCH=$(uname -m)
+if [[ "${CURRENT_ARCH}" == "aarch64" ]]; then
   INTERPRETER_PATH=/lib/ld-linux-aarch64.so.1
 else
   INTERPRETER_PATH=/lib64/ld-linux-x86-64.so.2
 fi
 
-# Patchelf the executable's interpreter
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}"/bin/ct_unwrapped
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}"/bin/db-backend
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}"/bin/db-backend-record
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}"/bin/backend-manager
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}"/bin/nargo
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}"/bin/wazero
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}"/bin/ctags
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}"/bin/curl
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}"/bin/cargo-stylus
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}"/bin/node
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${APP_DIR}"/ruby/bin/ruby
-
-# Clear up the executable's rpath
-patchelf --remove-rpath "${APP_DIR}"/bin/ct_unwrapped
-patchelf --remove-rpath "${APP_DIR}"/bin/db-backend
-patchelf --remove-rpath "${APP_DIR}"/bin/db-backend-record
-patchelf --remove-rpath "${APP_DIR}"/bin/backend-manager
-patchelf --remove-rpath "${APP_DIR}"/bin/nargo
-patchelf --remove-rpath "${APP_DIR}"/bin/wazero
-patchelf --remove-rpath "${APP_DIR}"/bin/ctags
-patchelf --remove-rpath "${APP_DIR}"/bin/curl
-patchelf --remove-rpath "${APP_DIR}"/bin/node
-patchelf --remove-rpath "${APP_DIR}"/ruby/bin/ruby
-
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}"/bin/node
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}"/bin/ct_unwrapped
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}"/bin/db-backend
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}"/bin/db-backend-record
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}"/bin/backend-manager
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}"/bin/nargo
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}"/bin/wazero
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}"/bin/ctags
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}"/bin/curl
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}"/bin/node
-patchelf --set-rpath "\$ORIGIN/../lib" "${APP_DIR}"/ruby/bin/ruby
-
-APPIMAGE_ARCH=$CURRENT_ARCH
-if [[ "$APPIMAGE_ARCH" == "aarch64" ]]; then
-  # The appimagetool has its own convention for specifying the ARM64 arch
+APPIMAGE_ARCH=${CURRENT_ARCH}
+if [[ "${APPIMAGE_ARCH}" == "aarch64" ]]; then
+  # The appimagetool has its own convention for specifying the ARM64 arch.
   APPIMAGE_ARCH=arm_aarch64
 fi
 
 # Use AppImage tool to create AppImage itself
-ARCH=$APPIMAGE_ARCH appimagetool "${APP_DIR}" CodeTracer.AppImage
+ARCH=${APPIMAGE_ARCH} appimagetool "${APP_DIR}" CodeTracer.AppImage
 
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${ROOT_PATH}"/CodeTracer.AppImage
-patchelf --remove-rpath "${ROOT_PATH}"/CodeTracer.AppImage
+patchelf --set-interpreter "${INTERPRETER_PATH}" "${ROOT_PATH}/CodeTracer.AppImage"
+patchelf --remove-rpath "${ROOT_PATH}/CodeTracer.AppImage"
 
 echo "============================"
 echo "AppImage successfully built!"
diff --git a/appimage-scripts/build_appimage2.sh b/appimage-scripts/build_appimage2.sh
deleted file mode 100755
index 97826f373..000000000
--- a/appimage-scripts/build_appimage2.sh
+++ /dev/null
@@ -1,88 +0,0 @@
-#!/usr/bin/env bash
-
-# THIS SCRIPT IS TO BE RUN IN OUR DEV SHELL
-
-# The goal of this script is to prepare an `AppDir` (see the spec below)
-# and then to launch the appimagetool to create an AppImage.
-#
-# AppDir spec: https://github.com/AppImage/AppImageSpec/blob/master/draft.md#appdir
-# appimagetool: https://github.com/AppImage/appimagetool
-echo "============================"
-echo "AppImage build start"
-echo "============================"
-set -euo pipefail
-
-cleanup() {
-  echo "Performing cleanup..."
-  if [ -d ./squashfs-root ]; then
-    chmod -R u+rwX ./squashfs-root >/dev/null 2>&1 || true
-    rm -rf ./squashfs-root
-  fi
-}
-
-trap cleanup EXIT
-
-ROOT_PATH=$(git rev-parse --show-toplevel)
-export ROOT_PATH
-
-APP_DIR="${ROOT_PATH}/squashfs-root"
-export APP_DIR
-
-if [ -e "${ROOT_PATH}/CodeTracer.AppImage" ]; then
-  chmod -f u+rw "${ROOT_PATH}/CodeTracer.AppImage" >/dev/null 2>&1 || true
-  rm -f "${ROOT_PATH}/CodeTracer.AppImage"
-fi
-
-if [ -d "${APP_DIR}" ]; then
-  chmod -R u+rwX "${APP_DIR}" >/dev/null 2>&1 || true
-  rm -rf "${APP_DIR}"
-fi
-mkdir -p "${APP_DIR}"
-
-# This environment variable controls where build artifacts and static resources end up.
-export NIX_CODETRACER_EXE_DIR="${APP_DIR}"
-
-CURRENT_NIX_SYSTEM=$(nix eval --impure --raw --expr 'builtins.currentSystem')
-APPIMAGE_PAYLOAD=$(nix build "${ROOT_PATH}#packages.${CURRENT_NIX_SYSTEM}.appimagePayload" --no-link --print-out-paths | tail -n1)
-
-cp -Lr "${APPIMAGE_PAYLOAD}/." "${APP_DIR}/"
-
-chmod -R u+rwX "${APP_DIR}"
-
-# Copy over electron
-# bash "${ROOT_PATH}/appimage-scripts/install_electron_nix.sh"
-bash "${ROOT_PATH}/appimage-scripts/install_electron.sh"
-
-# Setup node deps
-bash "${ROOT_PATH}/appimage-scripts/setup_node_deps.sh"
-
-cp -Lr "${ROOT_PATH}/src/public" "${APP_DIR}/public"
-chmod -R +wr "${APP_DIR}/public"
-mkdir -p "${APP_DIR}/public/dist"
-cp -Lr "${ROOT_PATH}/src/public/dist/frontend_bundle.js" "${APP_DIR}/frontend_bundle.js"
-
-
-chmod -R +x "${APP_DIR}/electron"
-
-CURRENT_ARCH=$(uname -m)
-if [[ "${CURRENT_ARCH}" == "aarch64" ]]; then
-  INTERPRETER_PATH=/lib/ld-linux-aarch64.so.1
-else
-  INTERPRETER_PATH=/lib64/ld-linux-x86-64.so.2
-fi
-
-APPIMAGE_ARCH=${CURRENT_ARCH}
-if [[ "${APPIMAGE_ARCH}" == "aarch64" ]]; then
-  # The appimagetool has its own convention for specifying the ARM64 arch.
-  APPIMAGE_ARCH=arm_aarch64
-fi
-
-# Use AppImage tool to create AppImage itself
-ARCH=${APPIMAGE_ARCH} appimagetool "${APP_DIR}" CodeTracer.AppImage
-
-patchelf --set-interpreter "${INTERPRETER_PATH}" "${ROOT_PATH}/CodeTracer.AppImage"
-patchelf --remove-rpath "${ROOT_PATH}/CodeTracer.AppImage"
-
-echo "============================"
-echo "AppImage successfully built!"
-echo "============================"
diff --git a/appimage-scripts/build_backend_manager.sh b/appimage-scripts/build_backend_manager.sh
deleted file mode 100644
index 34ffbfd74..000000000
--- a/appimage-scripts/build_backend_manager.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env bash
-
-# depends on env `$ROOT_PATH` and `$NIX_CODETRACER_EXE_DIR` and cargo/rust installed
-
-set -e
-
-echo "==========="
-echo "codetracer build: build backend-manager"
-echo "-----------"
-
-
-pushd "$ROOT_PATH/src/backend-manager"
-cargo build --release
-popd
-
-cp -rL "$ROOT_PATH/src/backend-manager/target/release/backend-manager" "${NIX_CODETRACER_EXE_DIR}/bin/backend-manager"
-
-echo "==========="
diff --git a/appimage-scripts/build_css.sh b/appimage-scripts/build_css.sh
deleted file mode 100755
index b5e147e5b..000000000
--- a/appimage-scripts/build_css.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/usr/bin/env bash
-
-# depends on env `$ROOT_PATH` and `$NIX_CODETRACER_EXE_DIR`
-# and node_modules setup
-
-set -e
-
-echo "==========="
-echo "codetracer build: build css"
-echo "-----------"
-
-pushd "$ROOT_PATH"
-
-mkdir -p "$NIX_CODETRACER_EXE_DIR/frontend/styles/"
-stylus=$ROOT_PATH/node_modules/.bin/stylus
-node "$stylus" -o "$NIX_CODETRACER_EXE_DIR/frontend/styles/" src/frontend/styles/default_white_theme.styl
-node "$stylus" -o "$NIX_CODETRACER_EXE_DIR/frontend/styles/" src/frontend/styles/default_dark_theme_electron.styl
-node "$stylus" -o "$NIX_CODETRACER_EXE_DIR/frontend/styles/" src/frontend/styles/loader.styl
-node "$stylus" -o "$NIX_CODETRACER_EXE_DIR/frontend/styles/" src/frontend/styles/subwindow.styl
-
-popd
-
-echo "==========="
diff --git a/appimage-scripts/build_db_backend.sh b/appimage-scripts/build_db_backend.sh
deleted file mode 100755
index 7940d6fda..000000000
--- a/appimage-scripts/build_db_backend.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/usr/bin/env bash
-
-# depends on env `$ROOT_PATH` and `$NIX_CODETRACER_EXE_DIR` and cargo/rust installed
-
-set -e
-
-echo "==========="
-echo "codetracer build: build db-backend"
-echo "-----------"
-
-
-pushd "$ROOT_PATH/src/db-backend"
-cargo build --release
-popd
-
-cp -rL "$ROOT_PATH/src/db-backend/target/release/db-backend" "${NIX_CODETRACER_EXE_DIR}/bin/db-backend"
-
-echo "==========="
diff --git a/appimage-scripts/build_with_nim.sh b/appimage-scripts/build_with_nim.sh
deleted file mode 100755
index 19ca8e22d..000000000
--- a/appimage-scripts/build_with_nim.sh
+++ /dev/null
@@ -1,118 +0,0 @@
-#!/usr/bin/env bash
-
-# depends on env `$ROOT_PATH` and `$NIX_CODETRACER_EXE_DIR`
-#   and nim 1.6 installed
-#   and valid env `$LIBSQLITE3_PATH` at least for nixos
-
-set -e
-
-echo "==========="
-echo "codetracer build: build based on nim"
-echo "-----------"
-
-pushd "$ROOT_PATH"
-
-echo "links path const:"
-echo "${APP_DIR}"
-
-
-    # --passL:"${APP_DIR}/lib/libsqlite3.so.0" \
-
-# codetracer
-nim -d:release \
-    --d:asyncBackend=asyncdispatch \
-    --dynlibOverride:std -d:staticStd \
-    --gc:refc --hints:on --warnings:off \
-    --dynlibOverride:"sqlite3" \
-    --dynlibOverride:"pcre" \
-    --dynlibOverride:"libzip" \
-    --dynlibOverride:"libcrypto" \
-    --dynlibOverride:"libssl" \
-    --passL:"-Wl,-Bstatic -lsqlite3 -Wl,-Bdynamic" \
-    --passL:"${APP_DIR}/lib/libpcre.so.1" \
-    --passL:"${APP_DIR}/lib/libzip.so.5" \
-    --passL:"${APP_DIR}/lib/libcrypto.so" \
-    --passL:"${APP_DIR}/lib/libcrypto.so.3" \
-    --passL:"${APP_DIR}/lib/libssl.so" \
-    --boundChecks:on \
-    -d:useOpenssl3 \
-    -d:ssl \
-    -d:chronicles_sinks=json -d:chronicles_line_numbers=true \
-    -d:chronicles_timestamps=UnixTime \
-    -d:ctTest -d:testing --hint"[XDeclaredButNotUsed]":off \
-    -d:builtWithNix \
-    -d:ctEntrypoint \
-    -d:linksPathConst=.. \
-    -d:libcPath=libc \
-    -d:pathToNodeModules=../node_modules \
-    --nimcache:nimcache \
-    --out:"${APP_DIR}/bin/ct_unwrapped" c ./src/ct/codetracer.nim
-
-
-nim \
-    -d:release -d:asyncBackend=asyncdispatch \
-    --gc:refc --hints:off --warnings:off \
-    --debugInfo --lineDir:on \
-    --boundChecks:on --stacktrace:on --linetrace:on \
-    -d:chronicles_sinks=json -d:chronicles_line_numbers=true \
-    -d:chronicles_timestamps=UnixTime \
-    -d:ssl \
-    -d:ctTest -d:testing --hint"[XDeclaredButNotUsed]":off \
-    -d:linksPathConst=.. \
-    -d:libcPath=libc \
-    -d:builtWithNix \
-    -d:ctEntrypoint \
-    --dynlibOverride:"libsqlite3" \
-    --dynlibOverride:"sqlite3" \
-    --dynlibOverride:"pcre" \
-    --dynlibOverride:"libzip" \
-    --passL:"-Wl,-Bstatic -lsqlite3 -Wl,-Bdynamic" \
-    --passL:"${APP_DIR}/lib/libpcre.so.1" \
-    --passL:"${APP_DIR}/lib/libzip.so.5" \
-    --nimcache:nimcache \
-    --out:"${APP_DIR}/bin/db-backend-record" c ./src/ct/db_backend_record.nim
-
-    # --passL:"-lsqlite3" \
-    #--passL:"${APPDIR}/lib/libcrypto.so.3" \
-    #--passL:"${APPDIR}/lib/libssl.so.3" \
-    # --passL:"${APP_DIR}/lib/libz.so.1" \
-
-# this works    --passL:/nix/store/f6afb4jw9g5f94ixw0jn6cl0ah4liy35-sqlite-3.45.3/lib/libsqlite3.so.0 \
-
-    # TODO conditional for nixos?--passL:$LIBSQLITE3_PATH
-    #
-# patchelf --set-rpath ${APP_DIR}/lib ${APP_DIR}/bin/ct
-
-
-# index.js
-nim \
-    --hints:on --warnings:off --sourcemap:on \
-    -d:ctIndex -d:chronicles_sinks=json \
-    -d:nodejs --out:"${APP_DIR}/index.js" js src/frontend/index.nim
-cp "${APP_DIR}/index.js" "${APP_DIR}/src/index.js"
-
-nim \
-    --hints:on --warnings:off --sourcemap:on \
-    -d:ctIndex -d:server -d:chronicles_sinks=json \
-    -d:nodejs --out:"${APP_DIR}/server_index.js" js src/frontend/index.nim
-cp "${APP_DIR}/server_index.js" "${APP_DIR}/src/server_index.js"
-
-# ui.js
-nim \
-    --hints:off --warnings:off \
-    -d:chronicles_enabled=off  \
-    -d:ctRenderer \
-    --out:"${APP_DIR}/ui.js" js src/frontend/ui_js.nim
-cp "${APP_DIR}/ui.js" "${APP_DIR}/src/ui.js"
-
-# subwindow.js
-nim \
-    --hints:off --warnings:off \
-    -d:chronicles_enabled=off  \
-    -d:ctRenderer \
-    --out:"${APP_DIR}/subwindow.js" js src/frontend/subwindow.nim
-cp "${APP_DIR}/subwindow.js" "${APP_DIR}/src/subwindow.js"
-
-popd
-
-echo "==========="
diff --git a/appimage-scripts/install_ruby.sh b/appimage-scripts/install_ruby.sh
deleted file mode 100755
index 69e855bd5..000000000
--- a/appimage-scripts/install_ruby.sh
+++ /dev/null
@@ -1,12 +0,0 @@
-#!/usr/bin/env bash
-
-APP_DIR="${APP_DIR:-.}"
-
-# Install Ruby
-RUBY="$(dirname "$(dirname "$(which ruby)")")"
-echo "${RUBY}"
-
-mkdir -p "${APP_DIR}/ruby"
-
-cp -Lr --no-preserve=ownership "${RUBY}"/* "${APP_DIR}"/ruby
-chmod -R +x "${APP_DIR}/ruby"
diff --git a/nix/packages/default.nix b/nix/packages/default.nix
index 773fc1dcd..ab8b51c6b 100644
--- a/nix/packages/default.nix
+++ b/nix/packages/default.nix
@@ -14,7 +14,9 @@
       rubyPkg = pkgs.ruby_3_3;
     in
     {
-      packages = rec {
+      packages =
+        let
+          rawPackages = rec {
         upstream-nim-codetracer = pkgs.buildPackages.nim1.overrideAttrs (_: {
           postInstallPhase = ''
             mv $out/nim $out/upstream-nim
@@ -150,7 +152,7 @@
 
           copy_libs() {
             for lib in "$@"; do
-              cp -n -L "$lib" "$out/lib/" || true
+              cp -n -L "$lib" "$out/lib/"
             done
           }
 
@@ -182,7 +184,7 @@
             for binary in "$@"; do
               lddtree -l "$binary" | grep /nix | grep -v glibc | while read -r dep; do
                 [ -f "$dep" ] || continue
-                cp -n -L "$dep" "$out/lib/" || true
+                cp -n -L "$dep" "$out/lib/"
               done
             done
           }
@@ -207,7 +209,8 @@
           patch_binary() {
             local bin=$1
             if file "$bin" | grep -q 'ELF'; then
-              patchelf --remove-rpath "$bin" || true
+              chmod u+w "$bin"
+              patchelf --remove-rpath "$bin"
               patchelf --set-interpreter "''${INTERPRETER_PATH}" "$bin"
               patchelf --set-rpath '$ORIGIN/../lib' "$bin"
             fi
@@ -215,10 +218,10 @@
 
           for bin in "$out/bin"/*; do
             [ -f "$bin" ] || continue
-            patch_binary "$bin" || true
+            patch_binary "$bin"
           done
 
-          patch_binary "$out/ruby/bin/ruby" || true
+          patch_binary "$out/ruby/bin/ruby"
         '';
 
         nimBuildInputs = [
@@ -480,7 +483,8 @@
           patch_binary() {
             local bin=$1
             if file "$bin" | grep -q 'ELF'; then
-              patchelf --remove-rpath "$bin" || true
+              chmod u+w "$bin"
+              patchelf --remove-rpath "$bin"
               patchelf --set-interpreter "''${INTERPRETER_PATH}" "$bin"
               patchelf --set-rpath '$ORIGIN/../lib' "$bin"
             fi
@@ -491,7 +495,7 @@
             local dest=$2
             cp -L "$src" "$out/bin/$(basename "$dest")"
             chmod +x "$out/bin/$(basename "$dest")"
-            patch_binary "$out/bin/$(basename "$dest")" || true
+            patch_binary "$out/bin/$(basename "$dest")"
           }
 
           install_bin ${db-backend}/bin/db-backend db-backend
@@ -514,7 +518,7 @@
           cat <<'EOF' > "$out/bin/ct"
 #!/usr/bin/env bash
 
-HERE=''${HERE:-$(dirname "$(readlink -f "$0")")}
+HERE=''${HERE:-$(dirname "$(readlink -f "$0")")/..}
 
 # TODO: This includes references to x86_64. What about aarch64?
 
@@ -561,9 +565,9 @@ EOF
 
           cp "''${SRC_ICONSET_DIR}/icon_256x256.png" "$out/codetracer.png"
 
-          patch_binary "$out/bin/ct_unwrapped" || true
-          patch_binary "$out/bin/db-backend-record" || true
-          patch_binary "$out/ruby/bin/ruby" || true
+          patch_binary "$out/bin/ct_unwrapped"
+          patch_binary "$out/bin/db-backend-record"
+          patch_binary "$out/ruby/bin/ruby"
         '';
 
         indexJavascript = stdenv.mkDerivation {
@@ -1123,5 +1127,12 @@ EOF
 
         default = codetracer;
       };
+        in
+        builtins.removeAttrs rawPackages [
+          "nimBuildInputs"
+          "nimBuildSetup"
+          "mkNimBinary"
+          "mkNimJs"
+        ];
     };
 }
diff --git a/node-packages/yarn-project.nix b/node-packages/yarn-project.nix
index d155f8bcb..299f9b832 100644
--- a/node-packages/yarn-project.nix
+++ b/node-packages/yarn-project.nix
@@ -1,21 +1,8 @@
 # This file is generated by running "yarn install" inside your project.
 # Manual changes might be lost - proceed with caution!
 
-{
-  lib,
-  stdenv,
-  nodejs,
-  git,
-  cacert,
-  fetchurl,
-  writeShellScript,
-  writeShellScriptBin,
-}:
-{
-  src,
-  overrideAttrs ? null,
-  ...
-}@args:
+{ lib, stdenv, nodejs, git, cacert, fetchurl, writeShellScript, writeShellScriptBin }:
+{ src, overrideAttrs ? null, ... } @ args:
 
 let
 
@@ -25,7 +12,8 @@ let
   lockfile = ./yarn.lock;
 
   # Call overrideAttrs on a derivation if a function is provided.
-  optionalOverride = fn: drv: if fn == null then drv else drv.overrideAttrs fn;
+  optionalOverride = fn: drv:
+    if fn == null then drv else drv.overrideAttrs fn;
 
   # Simple stub that provides the global yarn command.
   yarn = writeShellScriptBin "yarn" ''
@@ -35,10 +23,7 @@ let
   # Common attributes between Yarn derivations.
   drvCommon = {
     # Make sure the build uses the right Node.js version everywhere.
-    buildInputs = [
-      nodejs
-      yarn
-    ];
+    buildInputs = [ nodejs yarn ];
     # All dependencies should already be cached.
     yarn_enable_network = "0";
     # Tell node-gyp to use the provided Node.js headers for native code builds.
@@ -55,16 +40,9 @@ let
     export yarn_enable_nixify=false
   '';
 
-  cacheDrv = stdenv.mkDerivation rec {
+  cacheDrv = stdenv.mkDerivation {
     name = "yarn-cache";
-    buildInputs = [
-      yarn
-      git
-      cacert
-    ];
-
-    nativeBuildInputs = buildInputs ++ [ nodejs ];
-
+    buildInputs = [ yarn git cacert ];
     buildCommand = ''
       cp --reflink=auto --recursive '${src}' ./src
       cd ./src/
@@ -74,105 +52,96 @@ let
       rm $out/.gitignore
     '';
     outputHashMode = "recursive";
-    outputHash = (
-      if stdenv.isAarch64 then
-        "sha512-+f3z4zwF2YlzskL7uDwVvQ3Fg0EYJ1HGPEqIGNb2VsiQpXoY2tU+EufqX79YRCOW7lXkuDfMQHYI3XcPioAEvg=="
-      else
-        "sha512-8spVLTYEciHn5q0N1R4fRB9EBM4gzZ1Zd4EeZdLwQM6ob+wvgP3oMH6JHQXUxKraP8TlpuVg7l2gNsTaAH5NoQ=="
-    );
+    outputHash = "sha512-8spVLTYEciHn5q0N1R4fRB9EBM4gzZ1Zd4EeZdLwQM6ob+wvgP3oMH6JHQXUxKraP8TlpuVg7l2gNsTaAH5NoQ==";
   };
 
   # Main project derivation.
-  project = stdenv.mkDerivation (
-    drvCommon
-    // {
-      inherit src;
-      name = "codetracer";
-
-      configurePhase = ''
-        ${buildVars}
-
-        # Copy over the Yarn cache.
-        rm -fr '${cacheFolder}'
-        mkdir -p '${cacheFolder}'
-        cp --reflink=auto --recursive ${cacheDrv}/* '${cacheFolder}/'
-
-        # Yarn may need a writable home directory.
-        export yarn_global_folder="$TMP"
-
-        # Ensure global cache is disabled. Cache must be part of our output.
-        touch .yarnrc.yml
-        sed -i -e '/^enableGlobalCache/d' .yarnrc.yml
-        echo 'enableGlobalCache: false' >> .yarnrc.yml
-
-        # Some node-gyp calls may call out to npm, which could fail due to an
-        # read-only home dir.
-        export HOME="$TMP"
-
-        # running preConfigure after the cache is populated allows for
-        # preConfigure to contain substituteInPlace for dependencies as well as the
-        # main project. This is necessary for native bindings that maybe have
-        # hardcoded values.
-        runHook preConfigure
-
-        # Run normal Yarn install to complete dependency installation.
-        yarn install --immutable --immutable-cache
-
-        runHook postConfigure
-      '';
+  project = stdenv.mkDerivation (drvCommon // {
+    inherit src;
+    name = "codetracer";
 
-      buildPhase = ''
-        runHook preBuild
-        runHook postBuild
-      '';
+    configurePhase = ''
+      ${buildVars}
 
-      installPhase = ''
-        runHook preInstall
+      # Copy over the Yarn cache.
+      rm -fr '${cacheFolder}'
+      mkdir -p '${cacheFolder}'
+      cp --reflink=auto --recursive ${cacheDrv}/* '${cacheFolder}/'
 
-        # Move the package contents to the output directory.
-        if grep -q '"workspaces"' package.json; then
-          # We can't use `yarn pack` in a workspace setup, because it only
-          # packages the outer workspace.
-          mkdir -p "$out/libexec"
-          mv $PWD "$out/libexec/$name"
-        else
-          # - If the package.json has a `files` field, only files matching those patterns are copied
-          # - Otherwise all files are copied.
-          yarn pack --out package.tgz
-          mkdir -p "$out/libexec/$name"
-          tar xzf package.tgz --directory "$out/libexec/$name" --strip-components=1
+      # Yarn may need a writable home directory.
+      export yarn_global_folder="$TMP"
 
-          cp --reflink=auto .yarnrc* "$out/libexec/$name"
-          cp --reflink=auto ${lockfile} "$out/libexec/$name/yarn.lock"
-          cp --reflink=auto --recursive .yarn "$out/libexec/$name"
+      # Ensure global cache is disabled. Cache must be part of our output.
+      touch .yarnrc.yml
+      sed -i -e '/^enableGlobalCache/d' .yarnrc.yml
+      echo 'enableGlobalCache: false' >> .yarnrc.yml
 
-          # Copy the Yarn linker output into the package.
-          cp --reflink=auto --recursive node_modules "$out/libexec/$name"
-        fi
+      # Some node-gyp calls may call out to npm, which could fail due to an
+      # read-only home dir.
+      export HOME="$TMP"
 
-        cd "$out/libexec/$name"
+      # running preConfigure after the cache is populated allows for
+      # preConfigure to contain substituteInPlace for dependencies as well as the
+      # main project. This is necessary for native bindings that maybe have
+      # hardcoded values.
+      runHook preConfigure
 
-        # Invoke a plugin internal command to setup binaries.
-        mkdir -p "$out/bin"
-        yarn nixify install-bin $out/bin
+      # Run normal Yarn install to complete dependency installation.
+      yarn install --immutable --immutable-cache
 
-        # A package with node_modules doesn't need the cache
-        yarn cache clean
+      runHook postConfigure
+    '';
 
-        runHook postInstall
-      '';
+    buildPhase = ''
+      runHook preBuild
+      runHook postBuild
+    '';
+
+    installPhase = ''
+      runHook preInstall
 
-      passthru = {
-        inherit nodejs;
-        yarn-freestanding = yarn;
-        yarn = writeShellScriptBin "yarn" ''
-          exec '${yarn}/bin/yarn' --cwd '${overriddenProject}/libexec/${overriddenProject.name}' "$@"
-        '';
-      };
-    }
-  );
+      # Move the package contents to the output directory.
+      if grep -q '"workspaces"' package.json; then
+        # We can't use `yarn pack` in a workspace setup, because it only
+        # packages the outer workspace.
+        mkdir -p "$out/libexec"
+        mv $PWD "$out/libexec/$name"
+      else
+        # - If the package.json has a `files` field, only files matching those patterns are copied
+        # - Otherwise all files are copied.
+        yarn pack --out package.tgz
+        mkdir -p "$out/libexec/$name"
+        tar xzf package.tgz --directory "$out/libexec/$name" --strip-components=1
+
+        cp --reflink=auto .yarnrc* "$out/libexec/$name"
+        cp --reflink=auto ${lockfile} "$out/libexec/$name/yarn.lock"
+        cp --reflink=auto --recursive .yarn "$out/libexec/$name"
+
+        # Copy the Yarn linker output into the package.
+        cp --reflink=auto --recursive node_modules "$out/libexec/$name"
+      fi
+
+      cd "$out/libexec/$name"
+
+      # Invoke a plugin internal command to setup binaries.
+      mkdir -p "$out/bin"
+      yarn nixify install-bin $out/bin
+
+      # A package with node_modules doesn't need the cache
+      yarn cache clean
+
+      runHook postInstall
+    '';
+
+    passthru = {
+      inherit nodejs;
+      yarn-freestanding = yarn;
+      yarn = writeShellScriptBin "yarn" ''
+        exec '${yarn}/bin/yarn' --cwd '${overriddenProject}/libexec/${overriddenProject.name}' "$@"
+      '';
+    };
+  });
 
   overriddenProject = optionalOverride overrideAttrs project;
 
-in
-overriddenProject
+in overriddenProject