docs: update refactoring spec with submodule architecture
Enforces max 5-10 files per directory using proper subpackages:
- api/tool/, api/config/, api/workspace/, api/user/, api/project/, api/system/
- services/docker/, services/instance/, services/config/, services/git/,
services/build/, services/terminal/, services/shared/
- models/tool/, models/config/, models/user/, models/project/, models/system/
- schemas/tool/, schemas/config/, schemas/user/, schemas/project/, schemas/system/
Updated design.md module map and tasks.md with 9 phases.
alex
0127d283a6