diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index d42ff77..db3a344 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -13,10 +13,12 @@ jobs:
     - uses: actions/checkout@v4
     - name: ensure `./wit/deps` are in sync
       run: |
-        curl -Lo 'wit-deps' https://github.com/bytecodealliance/wit-deps/releases/download/v0.3.3/wit-deps-x86_64-unknown-linux-musl
+        curl -Lo 'wit-deps' https://github.com/bytecodealliance/wit-deps/releases/download/v0.5.0/wit-deps-x86_64-unknown-linux-musl
         chmod +x wit-deps
         ./wit-deps lock
+        ./wit-deps -m wit-0.3.0-draft/deps.toml -l wit-0.3.0-draft/deps.lock -d wit-0.3.0-draft/deps lock
         git add -N wit/deps
+        git add -N wit-0.3.0-draft/deps
         git diff --exit-code
     - uses: WebAssembly/wit-abi-up-to-date@v22
       with:
diff --git a/wit-0.3.0-draft/deps.lock b/wit-0.3.0-draft/deps.lock
index 20306c6..0386808 100644
--- a/wit-0.3.0-draft/deps.lock
+++ b/wit-0.3.0-draft/deps.lock
@@ -1,4 +1,5 @@
 [clocks]
 url = "https://github.com/WebAssembly/wasi-clocks/archive/main.tar.gz"
+subdir = "wit-0.3.0-draft"
 sha256 = "26e315db0d371495f8834edfc0e479042f94152ce677d96d54d3623d0e4ffb1e"
 sha512 = "e1c76f499435841316f9287b88d8173558e64f277c321ff390556de8707a0b18dd6c1749bbb17bbbba8d523da246ef6eb05c990ceddb762e03efb2ae30cacc76"
diff --git a/wit-0.3.0-draft/deps.toml b/wit-0.3.0-draft/deps.toml
index 3f6ad6d..e004547 100644
--- a/wit-0.3.0-draft/deps.toml
+++ b/wit-0.3.0-draft/deps.toml
@@ -1 +1 @@
-clocks = "https://github.com/WebAssembly/wasi-clocks/archive/main.tar.gz"
+clocks = { url = "https://github.com/WebAssembly/wasi-clocks/archive/main.tar.gz", subdir = "wit-0.3.0-draft" }
diff --git a/wit/deps.lock b/wit/deps.lock
index 316cbaa..0386808 100644
--- a/wit/deps.lock
+++ b/wit/deps.lock
@@ -1,9 +1,5 @@
 [clocks]
 url = "https://github.com/WebAssembly/wasi-clocks/archive/main.tar.gz"
-sha256 = "93a701968a7dd3c5d69031bc0601681c468972fdf7e28a93bb6150a67d6ebe8b"
-sha512 = "98fca567c7a01887b0fb38981f1772169b6ea8de475b546508f8b86738d84e44ba95cae81def40ac34e8809f5f60e85224077ab8cb6d6d5d6296acc1df73c159"
-
-[io]
-url = "https://github.com/WebAssembly/wasi-io/archive/main.tar.gz"
-sha256 = "1cccbfe4122686ea57a25cd368e8cdfc408cbcad089f47fb6685b6f92e96f050"
-sha512 = "7a95f964c13da52611141acd89bc8876226497f128e99dd176a4270c5b5efbd8cc847b5fbd1a91258d028c646db99e0424d72590cf1caf20f9f3a3343fad5017"
+subdir = "wit-0.3.0-draft"
+sha256 = "26e315db0d371495f8834edfc0e479042f94152ce677d96d54d3623d0e4ffb1e"
+sha512 = "e1c76f499435841316f9287b88d8173558e64f277c321ff390556de8707a0b18dd6c1749bbb17bbbba8d523da246ef6eb05c990ceddb762e03efb2ae30cacc76"