refactor: Restructure monorepo to apps/server/ and apps/web/ layout

Move src/ → apps/server/ and packages/web/ → apps/web/ to adopt
standard monorepo conventions (apps/ for runnable apps, packages/
for reusable libraries). Update all config files, shared package
imports, test fixtures, and documentation to reflect new paths.

Key fixes:
- Update workspace config to ["apps/*", "packages/*"]
- Update tsconfig.json rootDir/include for apps/server/
- Add apps/web/** to vitest exclude list
- Update drizzle.config.ts schema path
- Fix ensure-schema.ts migration path detection (3 levels up in dev,
  2 levels up in dist)
- Fix tests/integration/cli-server.test.ts import paths
- Update packages/shared imports to apps/server/ paths
- Update all docs/ files with new paths

docs/git-process-logging.md

@@ -2,7 +2,7 @@
 
 Three infrastructure modules supporting agent execution.
 
-## Git Module (`src/git/`)
+## Git Module (`apps/server/git/`)
 
 Manages git worktrees for isolated agent workspaces.
 
@@ -31,7 +31,7 @@ Worktrees stored in `.cw-worktrees/` subdirectory of the repo. Each agent gets a
 4. On conflict: `git merge --abort`, emit `worktree:conflict` with conflicting file list
 5. Restore original branch
 
-### BranchManager (`src/git/branch-manager.ts`)
+### BranchManager (`apps/server/git/branch-manager.ts`)
 - **Port**: `BranchManager` interface
 - **Adapter**: `SimpleGitBranchManager` using simple-git
 
@@ -56,7 +56,7 @@ Worktrees stored in `.cw-worktrees/` subdirectory of the repo. Each agent gets a
 
 ---
 
-## Process Module (`src/process/`)
+## Process Module (`apps/server/process/`)
 
 Spawns, tracks, and controls child processes.
 
@@ -85,13 +85,13 @@ Spawns, tracks, and controls child processes.
 
 ---
 
-## Logger Module (`src/logger/`)
+## Logger Module (`apps/server/logger/`)
 
 Structured logging via **pino**.
 
 ### Usage
 ```typescript
-import { createModuleLogger } from './logger/index.js';
+import { createModuleLogger } from '../logger/index.js';
 const log = createModuleLogger('my-module');
 log.info({ key: 'value' }, 'message');
 ```
@@ -109,7 +109,7 @@ log.info({ key: 'value' }, 'message');
 
 ---
 
-## Logging Module (`src/logging/`)
+## Logging Module (`apps/server/logging/`)
 
 File-based per-process output capture (separate from pino).