docs: update documentation for new build directory structure

- Add build locations section to AGENTS.md
- Update README.md with build directory information
- Fix AGENTS.md vm-run command reference
- Document that clean removes both ./build/ and ./result/
- Ensure consistency across all documentation files

Addresses documentation inconsistencies after Makefile changes.

AGENTS.md

@@ -44,7 +44,7 @@ This file provides guidelines for AI coding agents operating within this reposit
 
 1. Use `make vm-run` for local development
 2. Test with all 15 containers to match production
-3. Use `make usb-build` for workshop USB drives
+3. Use `make usb-build` for workshop USB drives (outputs to ./build/iso/)
 4. Deploy to cloud with `make deploy-cloud`
 
 ## General Guidelines
@@ -56,6 +56,12 @@ This file provides guidelines for AI coding agents operating within this reposit
 - Maintain feature parity between USB/VM environments where possible
 - **ALWAYS check package existence on search.nixos.org before adding new packages**
 
+## Build Locations
+
+- **USB ISOs**: `./build/iso/result/iso/*.iso` (custom build directory)
+- **VM builds**: `./result/` (Nix default symlink)
+- **Clean command**: Removes both `./build/` and `./result/` directories
+
 ## ⚠️ Critical Warnings
 
 - **NEVER RUN `nix-env`** - This can break your Nix environment. Use `nix-shell`, `nix develop`, or declarative approaches instead.