diff --git a/.github/workflows/builder-docker-image.yml b/.github/workflows/builder-docker-image.yml
index 12f42b730..4accd59d2 100644
--- a/.github/workflows/builder-docker-image.yml
+++ b/.github/workflows/builder-docker-image.yml
@@ -58,4 +58,4 @@ jobs:
         run: |
           cp .env.example .env
           sed -i -e "s|OSXCROSS_URL=http://example.com/osxcross/osxcross.tar.xz|OSXCROSS_URL=${{ secrets.OSXCROSS_URL }}|g" .env
-          ./docker-dev docker-image-build-push
+          ./docker/dev docker-image-build-push
diff --git a/.github/workflows/cli.yml b/.github/workflows/cli.yml
index befde428a..0d4cf127a 100644
--- a/.github/workflows/cli.yml
+++ b/.github/workflows/cli.yml
@@ -129,11 +129,11 @@ jobs:
 
       - name: "Build docker image (${{ matrix.arch }})"
         run: |
-          CROSS="${{ matrix.arch }}" ./docker-dev docker-image-build-push
+          CROSS="${{ matrix.arch }}" ./docker/dev docker-image-build-push
 
       - name: "Build CLI (${{ matrix.arch }})"
         run: |
-          CROSS="${{ matrix.arch }}" ./docker-dev build-release
+          CROSS="${{ matrix.arch }}" ./docker/dev build-release
 
       - name: "Upload build artifacts (${{ matrix.arch }})"
         uses: actions/upload-artifact@v4
@@ -185,7 +185,7 @@ jobs:
 
       - name: "Run unit tests"
         run: |
-          ./docker-dev test
+          ./docker/dev test
 
 
   run-lints:
@@ -231,7 +231,7 @@ jobs:
 
       - name: "Run lints"
         run: |
-          ./docker-dev lint-ci
+          ./docker/dev lint-ci
 
 
   run-smoke-tests:
diff --git a/.github/workflows/web.yml b/.github/workflows/web.yml
index 2947f94f9..5311f6af7 100644
--- a/.github/workflows/web.yml
+++ b/.github/workflows/web.yml
@@ -118,27 +118,27 @@ jobs:
 
       - name: "Build docker image"
         run: |
-          CROSS="wasm32-unknown-unknown" ./docker-dev docker-image-build-push
+          CROSS="wasm32-unknown-unknown" ./docker/dev docker-image-build-push
 
       - name: "Install Node.js packages"
         run: |
-          ./docker-dev web yarn install
+          ./docker/dev web yarn install
 
       - name: "Build WebAssembly module"
         run: |
-          ./docker-dev wasm-release
+          ./docker/dev wasm-release
 
       - name: "Build web app"
         run: |
-          ./docker-dev web-release
+          ./docker/dev web-release
 
       - name: "Lint web app code"
         run: |
-          ./docker-dev web yarn lint:ci
+          ./docker/dev web yarn lint:ci
 
       - name: "Lint Rust code"
         run: |
-          ./docker-dev lint-ci
+          ./docker/dev lint-ci
 
       - name: "Upload build artifacts"
         uses: actions/upload-artifact@v4
diff --git a/docker-cross b/docker/cross
similarity index 93%
rename from docker-cross
rename to docker/cross
index 599357f1e..e25a112a7 100755
--- a/docker-cross
+++ b/docker/cross
@@ -21,7 +21,7 @@ targets=(
 function run_one() {
   target=${1:?}
   printf "\nBuilding for %s\n" "${target}"
-  CROSS=${target} ./docker-dev br
+  CROSS=${target} ./docker/dev br
 }
 export -f run_one
 
diff --git a/docker-dev b/docker/dev
similarity index 95%
rename from docker-dev
rename to docker/dev
index fc8d69e62..6d900bcd7 100755
--- a/docker-dev
+++ b/docker/dev
@@ -7,52 +7,52 @@
 # (see dev guide).
 #
 # See the full list of possible commands in the long `case` block halfway through the script.
-# Here are some of the most useful ones:
+# Here are some of the most useful ones (run them from project root):
 #
 # * Build nextclade binary in debug mode:
-#   ./docker-dev b nextclade
+#   ./docker/dev b nextclade
 #
 # * Build nextclade binary in release mode:
-#   ./docker-dev br nextclade
+#   ./docker/dev br nextclade
 #
 # * Build and run nextclade binary in debug mode, with arguments:
-#   ./docker-dev r nextclade -- dataset list --help
+#   ./docker/dev r nextclade -- dataset list --help
 #
 # * Build and run nextclade binary in release mode, with arguments:
-#   ./docker-dev rr nextclade -- dataset list --help
+#   ./docker/dev rr nextclade -- dataset list --help
 #
 # * Cross-compile nextclade binary for Windows in release mode:
-#   CROSS=x86_64-pc-windows-gnu ./docker-dev br
+#   CROSS=x86_64-pc-windows-gnu ./docker/dev br
 #
 # * Build WebAssembly module in debug mode:
-#   ./docker-dev W
+#   ./docker/dev W
 #
 # * Build WebAssembly module in release mode:
-#   ./docker-dev Wr
+#   ./docker/dev Wr
 #
 # * Build and run web application in debug mode:
-#   ./docker-dev a
+#   ./docker/dev a
 #
 # * Build and run web application in release mode:
-#   ./docker-dev war
+#   ./docker/dev war
 #
 # * Lint Rust code:
-#   ./docker-dev l
+#   ./docker/dev l
 #
 # * Lint Rust code, apply automatic fixes:
-#   ./docker-dev lf
+#   ./docker/dev lf
 #
 # * Format Rust code:
-#   ./docker-dev f
+#   ./docker/dev f
 #
 # * Shell into the container:
-#   ./docker-dev bash
+#   ./docker/dev bash
 #
 # * Run arbitrary command inside the container:
-#   ./docker-dev cargo --version
+#   ./docker/dev cargo --version
 #
 # * Run arbitrary yarn command, in the context of web app, inside the container:
-#   ./docker-dev a yarn add --dev react
+#   ./docker/dev a yarn add --dev react
 #
 
 set -euo pipefail
@@ -75,7 +75,7 @@ HANDLE_SIGINT="trap \"${CANCELLED}; exit 0\" INT"
 export PACKAGE_NAME="nextclade"
 export PACKAGE_DIR_REL=""
 
-export PROJECT_ROOT_DIR="$(abspath "${THIS_DIR}")"
+export PROJECT_ROOT_DIR="$(abspath "${THIS_DIR}/..")"
 export PACKAGE_DIR="$(abspath "${PROJECT_ROOT_DIR}/${PACKAGE_DIR_REL}")"
 
 export DOCKER_REPO="nextstrain/nextclade_builder"
@@ -108,7 +108,7 @@ if [ -f "${PROJECT_ROOT_DIR}/.env" ]; then
   . "${PROJECT_ROOT_DIR}/.env"
 fi
 
-. "${THIS_DIR}/scripts/is_ci.sh"
+. "${PROJECT_ROOT_DIR}/scripts/is_ci.sh"
 
 export EXTENSIONS_TO_WATCH="rs,toml,lock"
 
diff --git a/scripts/docker_build_checksum.sh b/scripts/docker_build_checksum.sh
index c957d1f05..f096e4385 100755
--- a/scripts/docker_build_checksum.sh
+++ b/scripts/docker_build_checksum.sh
@@ -13,7 +13,7 @@ cat \
   .dockerignore \
   .gitignore \
   .nvmrc \
-  docker-dev \
+  docker/dev \
   docker/docker-dev.dockerfile \
   rust-toolchain.toml \
   scripts/docker_build_checksum.sh \