refactor: restructure workspace file organization (#121) (#122)

## Path Changes
- audit.log: memory/audit.log → log/audit.log
- projects.json: memory/projects.json → projects/projects.json
- prompts: roles/<project>/<role>.md → projects/prompts/<project>/<role>.md

## Files Updated
- lib/audit.ts - new audit log path
- lib/projects.ts - new projects.json path
- lib/dispatch.ts - new prompt instructions path
- lib/tools/project-register.ts - prompt scaffolding path
- lib/setup/workspace.ts - workspace scaffolding paths
- lib/context-guard.ts - projects.json path
- lib/tools/setup.ts - tool description
- lib/templates.ts - AGENTS.md template path references

## Documentation Updated
- README.md
- docs/ARCHITECTURE.md
- docs/ONBOARDING.md
- docs/QA_WORKFLOW.md
- docs/ROADMAP.md
- docs/TESTING.md

Addresses issue #121

lib/setup/workspace.ts

@@ -8,8 +8,6 @@ import path from "node:path";
 import {
   AGENTS_MD_TEMPLATE,
   HEARTBEAT_MD_TEMPLATE,
-  DEFAULT_DEV_INSTRUCTIONS,
-  DEFAULT_QA_INSTRUCTIONS,
 } from "../templates.js";
 
 /**
@@ -27,31 +25,19 @@ export async function scaffoldWorkspace(workspacePath: string): Promise<string[]
   await backupAndWrite(path.join(workspacePath, "HEARTBEAT.md"), HEARTBEAT_MD_TEMPLATE);
   filesWritten.push("HEARTBEAT.md");
 
-  // roles/default/dev.md and qa.md
-  const rolesDir = path.join(workspacePath, "roles", "default");
-  await fs.mkdir(rolesDir, { recursive: true });
-
-  const devRolePath = path.join(rolesDir, "dev.md");
-  if (!await fileExists(devRolePath)) {
-    await fs.writeFile(devRolePath, DEFAULT_DEV_INSTRUCTIONS, "utf-8");
-    filesWritten.push("roles/default/dev.md");
-  }
-
-  const qaRolePath = path.join(rolesDir, "qa.md");
-  if (!await fileExists(qaRolePath)) {
-    await fs.writeFile(qaRolePath, DEFAULT_QA_INSTRUCTIONS, "utf-8");
-    filesWritten.push("roles/default/qa.md");
-  }
-
-  // memory/projects.json
-  const memoryDir = path.join(workspacePath, "memory");
-  await fs.mkdir(memoryDir, { recursive: true });
-  const projectsJsonPath = path.join(memoryDir, "projects.json");
+  // projects/projects.json
+  const projectsDir = path.join(workspacePath, "projects");
+  await fs.mkdir(projectsDir, { recursive: true });
+  const projectsJsonPath = path.join(projectsDir, "projects.json");
   if (!await fileExists(projectsJsonPath)) {
     await fs.writeFile(projectsJsonPath, JSON.stringify({ projects: {} }, null, 2) + "\n", "utf-8");
-    filesWritten.push("memory/projects.json");
+    filesWritten.push("projects/projects.json");
   }
 
+  // log/ directory (audit.log created on first write)
+  const logDir = path.join(workspacePath, "log");
+  await fs.mkdir(logDir, { recursive: true });
+
   return filesWritten;
 }