chore: pause work and save context handoff

.planning/codebase/STRUCTURE.md

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+# Codebase Structure (`STRUCTURE.md`)
+
+## Directory Map
+
+- **Root Files**
+  - `bootstrap.bat` / `bootstrap.sh`: Primary runtime orchestrators for setting up the node/python environment.
+  - `.gitignore` & `.gitmodules`: Repository definitions protecting the ecosystem from pollution.
+  
+- **`.agent/` (The Enclave)**
+  - `.agent/env/`: The isolated local node environment container. Has its own `package.json` avoiding merging issues with user code.
+  - `.agent/scripts/`: Home of the Master Sync orchestration rules (`sync_vendors`, `extract_skills.js`, `translate_skills.js`).
+  - `.agent/skills/`: Holds the flattened markdown files (`SKILL.md`) that agents interpret on system boot. Note `gsd-*/` is whitelisted here.
+  - `.agent/vendor/`: The raw checked-out git repository targets before any translations/flattening is parsed out of them.
+  - `.agent/config/`: Runtime configurations specific to the current physical machine (`.env.agent`).
+  - `.agent/knowledge/`: Stores raw unstructured domain context for explicit queries.
+  
+- **`.planning/` (GSD Execution)**
+  - Manages the Project State (`PROJECT.md`, `ROADMAP.md`, `STATE.md`).
+  - `phases/`: Artifact history holding individual plans (`01-PLAN.md`) and the verification/summary reports mapping their outcomes.