update development setup with submodule, makefile, and docs

AGENTS.md

@@ -202,6 +202,15 @@ $: sound("hh*8").sometimes(rev).often(x => x.gain(0.5))
 - **Use NixOS shells/dev environments**: Always prefer Nix-based development environments for reproducible builds
 - **Current NixOS version**: 25.05
 
+#### Git Submodules
+
+The Strudel codebase is managed as a git submodule in the 'src' directory. To work with the codebase:
+
+1. Initialize submodules: `make submodules-init`
+2. Update submodules: `make submodules-update`
+
+This ensures the correct version of the Strudel repository is checked out and kept in sync.
+
 #### Nix Development Shell
 
 Use the following `flake.nix` for Strudel development:
@@ -257,9 +266,12 @@ Use the following `flake.nix` for Strudel development:
    ```
 
 **Option 2: Using Makefile (recommended)**
-The Makefile provides convenient shortcuts for common development tasks:
+The Makefile provides convenient shortcuts for common development tasks. First, ensure submodules are initialized:
 
 ```bash
+# Initialize and update submodules
+make update
+
 # Install dependencies
 make install