feat: eliminate deps/hyperlight-js git clone

Replace the manual git clone of hyperlight-js with Cargo's built-in
git dependency resolution. The runtime's Cargo.toml now uses a git dep
on hyperlight-js-runtime, and the NAPI addon (js-host-api) is built
from Cargo's checkout at ~/.cargo/git/checkouts/ with a symlink at
deps/js-host-api for npm file: dependency resolution.

Changes:
- Cargo git dep for hyperlight-js-runtime (was path dep to clone)
- HYPERLIGHT_CFLAGS resolved via cargo metadata + Node.js one-liner
- Justfile: resolve-hyperlight-dir discovers checkout, builds NAPI
  addon, creates symlink (no more fetch-hyperlight/git clone)
- package.json: file:deps/js-host-api (was file:deps/hyperlight-js/...)
- Scripts/tests: all paths updated to deps/js-host-api
- extract-hyperlight-builtins.ts: uses cargo metadata to find source
- Removed: jq dependency, build-with-runtime alias, dead PWD variable
- Docs: all clone references removed, setup descriptions updated
- Docker/CI: COPY path and comments updated for symlink pattern

Signed-off-by: Simon Davies <simongdavies@users.noreply.github.com>

Author: simongdavies

.claude/CLAUDE.md

@@ -36,7 +36,7 @@ Use `just` commands for development (preferred) or npm scripts:
 
 ```bash
 # ── Development ──
-just setup         # First-time setup: clone deps, build native addons, npm install
+just setup         # First-time setup: build native addons, npm install
 just build         # Rebuild native addons and install deps
 just start         # Run agent (tsx src/agent/index.ts)
 

.dockerignore

@@ -13,8 +13,6 @@ tests/
 .claude/
 
 # Rust build artifacts (huge - 9GB+)
-deps/hyperlight-js/target/
-src/hyperlight-analysis-guest/target/
 **/target/
 
 # KEEP dist/lib/node_modules (bundled @github/copilot SDK)

.github/copilot-instructions.md

@@ -29,7 +29,7 @@ Key config files at root: `package.json`, `tsconfig.json`, `vitest.config.ts`, `
 Always use these commands in this order for a clean build:
 
 ```bash
-just setup         # First-time only: clone deps, build native addons, npm install
+just setup         # First-time only: build native addons, npm install
 just build         # Rebuild native addons and install deps (run after Rust changes)
 ```
 

.github/workflows/pr-validate.yml

@@ -146,7 +146,7 @@ jobs:
           path: dist/
           retention-days: 7
 
-  # Build Docker image (just setup clones deps so Dockerfile COPY works)
+  # Build Docker image (just setup builds deps + creates symlinks for Dockerfile COPY)
   build-docker:
     name: Build Docker Image
     needs: [docs-pr]

CLAUDE.md

@@ -36,7 +36,7 @@ Use `just` commands for development (preferred) or npm scripts:
 
 ```bash
 # ── Development ──
-just setup         # First-time setup: clone deps, build native addons, npm install
+just setup         # First-time setup: build native addons, npm install
 just build         # Rebuild native addons and install deps
 just start         # Run agent (tsx src/agent/index.ts)
 

Dockerfile

@@ -27,8 +27,8 @@ WORKDIR /build
 # Copy package files first for layer caching
 COPY package*.json ./
 
-# Copy the hyperlight deps (for file: dependency)
-COPY deps/hyperlight-js/src/js-host-api/ ./deps/hyperlight-js/src/js-host-api/
+# Copy the NAPI addon (symlink created by `just setup`, BuildKit follows it)
+COPY deps/js-host-api/ ./deps/js-host-api/
 COPY src/code-validator/guest/ ./src/code-validator/guest/
 
 # Install dependencies

Justfile

@@ -9,26 +9,22 @@
 #   - KVM support (for running the Hyperlight micro-VM)
 #
 # First-time setup:
-#   just setup       # clones + builds hyperlight-js, installs npm deps
+#   just setup       # builds native addons, installs npm deps
 #
 # ─────────────────────────────────────────────────────────────────────
 
-# Windows: use PowerShell, replace backslashes for clang compatibility
+# Windows: use PowerShell
 set windows-shell := ["pwsh.exe", "-NoLogo", "-Command"]
 
-# In windows we need to replace the backslashes with forward slashes
-# otherwise clang will misinterpret the paths
-PWD := replace(justfile_dir(), "\\", "/")
-
 # On Windows, use Ninja generator for CMake to avoid aws-lc-sys build issues
 export CMAKE_GENERATOR := if os() == "windows" { "Ninja" } else { "" }
 
-# The hyperlight-js repo URL and ref to build against.
-# Currently using Simon's fork with in-flight PRs (binary types, call stats).
-# TODO: Switch to hyperlight-dev/hyperlight-js main once PRs land upstream.
-hyperlight-repo   := "https://github.com/simongdavies/hyperlight-js.git"
-hyperlight-ref    := "hyperagent"
-hyperlight-dir    := justfile_dir() / "deps" / "hyperlight-js"
+# The hyperlight-js workspace root, discovered from Cargo's git checkout.
+# The runtime's Cargo.toml uses a git dep on hyperlight-js-runtime, so Cargo
+# already clones the full workspace — we reuse that checkout to build the
+# NAPI addon (js-host-api) without a separate git clone.
+# Resolved lazily by the resolve-hyperlight-dir recipe.
+hyperlight-link   := justfile_dir() / "deps" / "js-host-api"
 
 # Hyperlight analysis guest (secure code validation in micro-VM)
 analysis-guest-dir := justfile_dir() / "src" / "code-validator" / "guest"
@@ -37,10 +33,10 @@ analysis-guest-dir := justfile_dir() / "src" / "code-validator" / "guest"
 runtime-dir := justfile_dir() / "src" / "sandbox" / "runtime"
 
 # HYPERLIGHT_CFLAGS needed for building guests that link rquickjs/QuickJS:
-# -I include/ provides stubs for the hyperlight target (no libc)
-# -D__wasi__=1 disables pthread support in QuickJS
-# Uses forward slashes (PWD) so clang works on Windows
-runtime-cflags := "-I" + PWD + "/deps/hyperlight-js/src/hyperlight-js-runtime/include -D__wasi__=1"
+# The hyperlight target has no libc, so QuickJS needs stub headers plus
+# -D__wasi__=1 to disable pthreads. Uses cargo metadata to find the
+# include/ dir from the hyperlight-js-runtime dependency.
+runtime-cflags := `node -e "try{var m=JSON.parse(require('child_process').execSync('cargo +1.89 metadata --format-version 1 --manifest-path src/sandbox/runtime/Cargo.toml',{encoding:'utf8',stdio:['pipe','pipe','pipe']}));var p=m.packages.find(function(p){return p.name==='hyperlight-js-runtime'});if(p)console.log('-I'+require('path').join(require('path').dirname(p.manifest_path),'include')+' -D__wasi__=1')}catch(e){}" 2>/dev/null || echo ""`
 
 # Export HYPERLIGHT_CFLAGS so cargo-hyperlight picks them up when building runtimes
 export HYPERLIGHT_CFLAGS := runtime-cflags
@@ -50,12 +46,29 @@ export HYPERLIGHT_CFLAGS := runtime-cflags
 # Without this, the default runtime (no ha:ziplib) would be embedded.
 export HYPERLIGHT_JS_RUNTIME_PATH := runtime-dir / "target" / "x86_64-hyperlight-none" / "release" / "hyperagent-runtime"
 
-# Clone (or update) the hyperlight-js dependency at the pinned ref.
-# Cross-platform: - prefix ignores clone failure (dir already exists).
+# Resolve the hyperlight-js workspace root from Cargo's git checkout.
+# Uses cargo metadata to find where hyperlight-js-runtime lives, then
+# derives the workspace src/ dir (js-host-api is a sibling crate).
+# Outputs the workspace root path (parent of src/).
 [private]
-fetch-hyperlight:
-    -git clone --branch "{{hyperlight-ref}}" --single-branch --depth 1 "{{hyperlight-repo}}" "{{hyperlight-dir}}"
-    cd "{{hyperlight-dir}}" && git fetch origin "{{hyperlight-ref}}" --depth 1 && git checkout FETCH_HEAD
+[unix]
+resolve-hyperlight-dir:
+    #!/usr/bin/env bash
+    set -euo pipefail
+    dir=$(node -e "\
+      var m=JSON.parse(require('child_process').execSync(\
+        'cargo +1.89 metadata --format-version 1 --manifest-path src/sandbox/runtime/Cargo.toml',\
+        {encoding:'utf8',stdio:['pipe','pipe','pipe'],maxBuffer:20*1024*1024}));\
+      var p=m.packages.find(function(p){return p.name==='hyperlight-js-runtime'});\
+      if(p)console.log(require('path').resolve(require('path').dirname(p.manifest_path),'..','..'));\
+      else{process.stderr.write('hyperlight-js-runtime not found in cargo metadata');process.exit(1)}")
+    js_host_api="${dir}/src/js-host-api"
+    if [ ! -d "$js_host_api" ]; then
+      echo "❌ js-host-api not found at ${js_host_api}"
+      echo "   Run: cargo +1.89 fetch --manifest-path src/sandbox/runtime/Cargo.toml"
+      exit 1
+    fi
+    echo "$dir"
 
 # Install required Rust toolchains and cargo subcommands.
 # Cross-platform (Linux/macOS/Windows) — no bash required.
@@ -65,19 +78,25 @@ ensure-tools:
     rustup toolchain install 1.89 --no-self-update
     rustup toolchain install nightly --no-self-update
 
-# Build the native hyperlight-js NAPI addon (debug — default)
-# Depends on build-runtime-release so the custom runtime with native modules
-# is always embedded. cargo clean -p prevents stale cached builds.
+# Build the native hyperlight-js NAPI addon.
+# 1. Builds the custom runtime (Cargo git dep fetches hyperlight-js automatically)
+# 2. Discovers the hyperlight-js workspace from Cargo's checkout
+# 3. Builds the NAPI addon with our custom runtime embedded
+# 4. Symlinks deps/js-host-api → checkout/src/js-host-api for npm file: dep
 [private]
-build-hyperlight: fetch-hyperlight (build-runtime-release)
-    -cd "{{hyperlight-dir}}/src/hyperlight-js" && cargo clean -p hyperlight-js
-    cd "{{hyperlight-dir}}" && just build
-
-# Build the native hyperlight-js NAPI addon (release — optimised)
-[private]
-build-hyperlight-release: fetch-hyperlight (build-runtime-release)
-    -cd "{{hyperlight-dir}}/src/hyperlight-js" && cargo clean -p hyperlight-js
-    cd "{{hyperlight-dir}}" && just build release
+[unix]
+build-hyperlight target="debug": (build-runtime-release)
+    #!/usr/bin/env bash
+    set -euo pipefail
+    hl_dir=$(just resolve-hyperlight-dir)
+    # Clean stale hyperlight-js builds so build.rs re-embeds the runtime
+    cd "${hl_dir}/src/hyperlight-js" && cargo clean -p hyperlight-js 2>/dev/null || true
+    # Build the NAPI addon (inherits HYPERLIGHT_JS_RUNTIME_PATH from env)
+    cd "${hl_dir}" && just build {{ if target == "debug" { "" } else { target } }}
+    # Symlink for npm file: dependency resolution
+    mkdir -p "{{justfile_dir()}}/deps"
+    ln -sfn "${hl_dir}/src/js-host-api" "{{hyperlight-link}}"
+    echo "🔗 deps/js-host-api → ${hl_dir}/src/js-host-api"
 
 # Build the hyperlight-analysis-guest NAPI addon (debug)
 [private]
@@ -89,19 +108,19 @@ build-analysis-guest:
 build-analysis-guest-release:
     cd "{{analysis-guest-dir}}" && just build release && just build-napi release
 
-# Install npm deps (links hyperlight-js and analysis-guest from local dirs)
+# Install npm deps (builds native addons, symlinks js-host-api)
 [private]
-install: build-hyperlight build-analysis-guest
+install: (build-hyperlight) build-analysis-guest
     npm install
 
 # Install npm deps with release-built native addons
 [private]
-install-release: build-hyperlight-release build-analysis-guest-release
+install-release: (build-hyperlight "release") build-analysis-guest-release
     npm install
 
 # ── First-time setup ─────────────────────────────────────────────────
 
-# Clone hyperlight-js, build native addon, install npm deps
+# First-time setup: build native addons, install npm deps
 setup: ensure-tools install
     @echo "✅ Setup complete — run 'just start' to launch the agent"
 
@@ -187,18 +206,13 @@ test-analysis-guest:
 # ── HyperAgent Runtime (native modules) ──────────────────────────────
 
 # Build the custom runtime for the hyperlight target (debug)
-build-runtime: fetch-hyperlight
+build-runtime:
     cd "{{runtime-dir}}" && cargo +1.89 hyperlight build --target-dir target
 
 # Build the custom runtime for the hyperlight target (release)
-build-runtime-release: fetch-hyperlight
+build-runtime-release:
     cd "{{runtime-dir}}" && cargo +1.89 hyperlight build --target-dir target --release
 
-# Legacy alias — the standard build now always uses the custom runtime.
-# Kept for backwards compatibility with existing scripts/docs.
-build-with-runtime: build
-    @echo "✅ (build-with-runtime is now a no-op — 'just build' always uses the custom runtime)"
-
 # Lint Rust code in the custom runtime
 lint-runtime:
     cd "{{runtime-dir}}" && cargo +1.89 clippy --workspace -- -D warnings
@@ -238,7 +252,7 @@ check: lint-all test-all
 clean:
     rm -rf dist node_modules
 
-# Clean everything including the hyperlight-js clone
+# Clean everything including deps/ symlinks
 clean-all: clean
     rm -rf deps
 

README.md

@@ -125,7 +125,7 @@ Requires Node.js 22+, Rust toolchain, and [just](https://github.com/casey/just)
 git clone https://github.com/hyperlight-dev/hyperagent.git
 cd hyperagent
 
-# First-time setup — clones deps, builds native Rust addons, installs npm packages
+# First-time setup — builds native Rust addons, installs npm packages
 just setup
 
 # Run the agent (tsx transpiles on the fly — no build step needed)
@@ -140,7 +140,7 @@ Key `just` commands:
 
 | Command | What it does |
 |---------|-------------|
-| `just setup` | First-time setup (clone deps, build native addons, npm install) |
+| `just setup` | First-time setup (build native addons, npm install) |
 | `just build` | Rebuild native addons after Rust changes |
 | `just start` | Run agent with tsx (fast iteration) |
 | `just binary-release` | Build optimised standalone binary to `dist/bin/hyperagent` |

docs/DEVELOPMENT.md

@@ -12,20 +12,17 @@ For contribution guidelines (issues, PRs, DCO), see [CONTRIBUTING.md](../CONTRIB
 - **just** command runner (`cargo install just`)
 - **GitHub CLI** (`gh`) authenticated
 
-## Clone and Build
+## Build
 
 ```bash
 git clone https://github.com/hyperlight-dev/hyperagent
 cd hyperagent
 
-# Install Node dependencies
-npm install
-
-# Build native Hyperlight components
-just build
+# First-time setup — builds native addons, installs npm deps
+just setup
 
 # Verify setup
-npm test
+just test
 ```
 
 ## Running from Source