Thanks for the warm words, stewardsencha.
As for directory structure, I have been making it up as I go, starting from the default directory structure given by Architect.
My ExtJS4 project structure:
/app - all app files (e.g. '/app/controller', '/app/model', etc.)
/build - all build files, such as app-all.js, all-classes.js, etc.
/lib - all third party files, some in subfolders for organization
/extensions - all extjs overrides or extensions
/extjs - extjs builds
/src - extjs source files
/metadata - created by Architect
/fonts - web fonts
/sass - I use compass, so all .scss files and builds go here.
/statics - static html files for my project
/support - Jenkins(Continuous Integration) files
All index-(build | test | dev | prod) files are in root, along with my-project.jsb3 and some Architect files.
That's been working out well for me for now.