refactor(software): flatten registry/ into top-level software/ and toolchain/

Author: NathanFlurry

.github/workflows/bench.yml

@@ -29,7 +29,7 @@ jobs:
       - run: cargo build --release -p agentos-native-sidecar
       - run: cargo build --release -p agentos-native-baseline
       - run: cargo build --release --target wasm32-wasip1 -p agentos-native-baseline
-      - run: make -C registry/native commands
+      - run: make -C toolchain commands
       - run: node packages/runtime-core/scripts/copy-wasm-commands.mjs --require
       - run: pnpm --dir packages/runtime-core build
       - run: pnpm --dir packages/runtime-benchmarks bench:check

.github/workflows/ci-nightly.yml

@@ -23,7 +23,7 @@ jobs:
         with:
           targets: wasm32-wasip1
       - run: pnpm install --frozen-lockfile
-      - run: make -C registry/native commands
+      - run: make -C toolchain commands
       - run: node packages/runtime-core/scripts/copy-wasm-commands.mjs --require
       - run: cargo check --workspace
       - run: cargo clippy --workspace --all-targets -- -D warnings

.github/workflows/ci.yml

@@ -42,6 +42,7 @@ jobs:
       - run: node scripts/check-agentos-client-protocol-compat.mjs
       - run: node --test scripts/verify-fixed-versions.test.mjs
       - run: node scripts/verify-fixed-versions.mjs
+      - run: pnpm check-layout
       - run: cargo fmt --check
       - run: pnpm check-types
       - run: pnpm lint
@@ -63,10 +64,10 @@ jobs:
           targets: wasm32-wasip1
       - uses: Swatinem/rust-cache@v2
         with:
-          workspaces: registry/native -> registry/native/target
-          key: wasm-commands-${{ hashFiles('registry/native/Cargo.lock') }}
+          workspaces: toolchain -> toolchain/target
+          key: wasm-commands-${{ hashFiles('toolchain/Cargo.lock') }}
       - run: pnpm install --frozen-lockfile --filter '@rivet-dev/agentos-runtime-core...'
-      - run: make -C registry/native commands
+      - run: make -C toolchain commands
       - run: node packages/runtime-core/scripts/copy-wasm-commands.mjs --require
       - uses: actions/upload-artifact@v4
         with:

.github/workflows/publish.yaml

@@ -66,10 +66,10 @@ jobs:
           targets: wasm32-wasip1
       - uses: Swatinem/rust-cache@v2
         with:
-          workspaces: registry/native -> registry/native/target
-          key: wasm-commands-${{ hashFiles('registry/native/Cargo.lock') }}
+          workspaces: toolchain -> toolchain/target
+          key: wasm-commands-${{ hashFiles('toolchain/Cargo.lock') }}
       - run: pnpm install --frozen-lockfile --filter '@rivet-dev/agentos-runtime-core...'
-      - run: make -C registry/native commands
+      - run: make -C toolchain commands
       - run: node packages/runtime-core/scripts/copy-wasm-commands.mjs --require
       - uses: actions/upload-artifact@v4
         with:

Cargo.toml

@@ -1,5 +1,6 @@
 [workspace]
 resolver = "2"
+exclude = ["software"]
 members = [
     "crates/agentos-protocol",
     "crates/agentos-sidecar-core",

crates/client/tests/common/mod.rs

@@ -150,7 +150,7 @@ fn wasm_command_mounts() -> Vec<MountConfig> {
 /// Locate the materialized coreutils package under the in-repo registry build.
 pub fn coreutils_package_dir() -> Option<PathBuf> {
     let registry_dir = PathBuf::from(env!("CARGO_MANIFEST_DIR"))
-        .join("../../registry/software/coreutils/dist/package");
+        .join("../../software/coreutils/dist/package");
     if registry_dir.join("agentos-package.json").is_file() {
         return std::fs::canonicalize(registry_dir).ok();
     }
@@ -175,7 +175,7 @@ pub fn coreutils_wasm_dir() -> Option<PathBuf> {
     }
 
     let legacy_registry_dir =
-        PathBuf::from(env!("CARGO_MANIFEST_DIR")).join("../../registry/software/coreutils/wasm");
+        PathBuf::from(env!("CARGO_MANIFEST_DIR")).join("../../software/coreutils/wasm");
     if legacy_registry_dir.is_dir() {
         return std::fs::canonicalize(legacy_registry_dir).ok();
     }
@@ -244,6 +244,6 @@ pub async fn require_wasm_commands(os: &AgentOs, test_name: &str) -> bool {
         eprintln!("skipping {message}");
         false
     } else {
-        panic!("{message}; run the registry/native command build or set AGENT_OS_CLIENT_ALLOW_E2E_SKIPS=1 for local skip-only runs");
+        panic!("{message}; run the toolchain command build or set AGENT_OS_CLIENT_ALLOW_E2E_SKIPS=1 for local skip-only runs");
     }
 }

crates/client/tests/packages_aospkg_e2e.rs

@@ -16,7 +16,7 @@ mod common;
 fn coreutils_aospkg() -> Option<PathBuf> {
     for path in [
         PathBuf::from(env!("CARGO_MANIFEST_DIR"))
-            .join("../../registry/software/coreutils/dist/package.aospkg"),
+            .join("../../software/coreutils/dist/package.aospkg"),
         PathBuf::from(env!("CARGO_MANIFEST_DIR"))
             .join("../../node_modules/@agentos-software/coreutils/dist/package.aospkg"),
     ] {

crates/client/tests/pi_session_e2e.rs

@@ -9,7 +9,7 @@
 //! - `AGENT_OS_PI_MODULE_CWD` env (a workspace with a built/installed `@agentos-software/pi`), else
 //! - the repo root, but only when the in-repo adapter is built
 //!   (`node_modules/@agentos-software/pi/dist/adapter.js`). Build it with `pnpm --dir packages/core
-//!   build && pnpm --dir registry/agent/pi build` (core first for types).
+//!   build && pnpm --dir software/pi build` (core first for types).
 //!
 //! Background: a real agent SDK exercises module-loading patterns (tsc `__exportStar` CJS barrels,
 //! deep pnpm symlink graphs, `__dirname` package self-location) that mock ACP adapters never touch.
@@ -55,11 +55,11 @@ fn pi_module_cwd() -> Option<String> {
 
 fn pi_package_path() -> Option<PathBuf> {
     // Prefer the packed .aospkg — the artifact the registry actually ships.
-    let aospkg = repo_root().join("registry/agent/pi/dist/package.aospkg");
+    let aospkg = repo_root().join("software/pi/dist/package.aospkg");
     if aospkg.is_file() {
         return std::fs::canonicalize(aospkg).ok();
     }
-    let dir = repo_root().join("registry/agent/pi/dist/package");
+    let dir = repo_root().join("software/pi/dist/package");
     if dir.join("agentos-package.json").is_file() {
         std::fs::canonicalize(dir).ok()
     } else {

crates/client/tests/shell_pty_packages_e2e.rs

@@ -17,7 +17,7 @@ fn coreutils_package_path() -> Option<PathBuf> {
     // Prefer the packed .aospkg — the artifact registry packages actually ship.
     for aospkg in [
         PathBuf::from(env!("CARGO_MANIFEST_DIR"))
-            .join("../../registry/software/coreutils/dist/package.aospkg"),
+            .join("../../software/coreutils/dist/package.aospkg"),
         PathBuf::from(env!("CARGO_MANIFEST_DIR"))
             .join("../../node_modules/@agentos-software/coreutils/dist/package.aospkg"),
     ] {
@@ -27,7 +27,7 @@ fn coreutils_package_path() -> Option<PathBuf> {
     }
     for dir in [
         PathBuf::from(env!("CARGO_MANIFEST_DIR"))
-            .join("../../registry/software/coreutils/dist/package"),
+            .join("../../software/coreutils/dist/package"),
         PathBuf::from(env!("CARGO_MANIFEST_DIR"))
             .join("../../node_modules/@agentos-software/coreutils/dist/package"),
     ] {

crates/execution/CLAUDE.md

@@ -91,7 +91,7 @@ ESM loader hooks (`loader.mjs`) and CJS `Module._load` patches (`runner.mjs`) ar
 - Node-facing `readdir` results must filter `.`/`..`.
 - Async methods should dispatch under `fs.promises.*`.
 - `fs.promises` methods that need real concurrency must use dedicated async bridge globals in `packages/build-tools/bridge-src/`; wrapping `fs.*Sync` inside `async` functions still serializes `Promise.all(...)` behind the first sidecar response.
-- When adding WASI guest imports in `registry/native/crates/wasi-ext`, mirror the required module/object in `crates/execution/src/node_import_cache.rs`'s inline `NODE_WASM_RUNNER_SOURCE`; missing modules fail at `WebAssembly.instantiate()` before guest `main()` runs.
+- When adding WASI guest imports in `toolchain/crates/wasi-ext`, mirror the required module/object in `crates/execution/src/node_import_cache.rs`'s inline `NODE_WASM_RUNNER_SOURCE`; missing modules fail at `WebAssembly.instantiate()` before guest `main()` runs.
 - Keep the embedded WASI shim in `crates/execution/src/wasm.rs` aligned with the patched wasi-libc surface used by the C command suite; overrides like `fcntl(F_SETFL)` now depend on `fd_fdstat_set_flags`, and missing imports fail at instantiation time before the guest command can do real work.
 - The shared-V8 WASM runner now resolves its own module loads plus internal guest `fs.openSync` / `fs.readSync` / `fs.writeSync` / `fs.closeSync` traffic inside `crates/execution/src/wasm.rs`; if the embedded runner gains more internal file syscalls, extend that internal sync-RPC handling there instead of surfacing those requests to callers or reintroducing a host-Node runtime path.
 - fd-based APIs (`open`, `read`, `write`, `close`, `fstat`) plus `createReadStream`/`createWriteStream` should ride the same bridge.