feat: Add VM manifest system and code clarity improvements

Implement VM configuration manifest system compatible with security-pcc's
VMBundle.Config format, storing VM settings in config.plist.

**Manifest System:**
- Add VPhoneVirtualMachineManifest.swift with security-pcc compatible structure
- Add scripts/vm_manifest.py for manifest generation during vm_new
- Update VPhoneCLI to support --config option with CLI overrides
- Update vm_create.sh to generate config.plist with CPU/memory/screen settings

**Environment Variables:**
- CPU/MEMORY/DISK_SIZE now only used during vm_new (written to manifest)
- boot/boot_dfu automatically read from config.plist
- Remove unused CFW_INPUT variable (overridden by scripts internally)
- Document remaining variables with their usage scope

**Documentation:**
- Update README.md with VM configuration section
- Update docs/README_{zh,ja,ko}.md with translated VM configuration docs
- Update Makefile help output with vm_new options and config.plist usage
- Fix fw_patch_jb description: "dev + JB extensions"
- Fix restore_get_shsh description: "Dump SHSH response from Apple"

**Code Quality:**
- Add VPhoneVirtualMachineRefactored.swift demonstrating code-clarity principles
- Extract 200+ line init into focused configuration methods
- Improve naming: hardwareModel, graphicsConfiguration, soundDevice
- Add BatteryConnectivity enum for magic numbers
- Create research/manifest_and_refactoring_summary.md with full analysis

**Compatibility with security-pcc:**
- Platform type: Fixed vresearch101 (iPhone-only)
- Network: NAT only (no bridging/host-only needed)
- Added: ScreenConfig and SEP storage (iPhone-specific)
- Removed: VirtMesh plugin support (PCC-specific)

docs: add machineIdentifier storage analysis

Research and validate the integration of machineIdentifier into config.plist.

**Findings:**
- security-pcc stores machineIdentifier in config.plist (same approach)
- VZMacAuxiliaryStorage creation is independent of machineIdentifier
- VZMacMachineIdentifier only requires Data representation, not file source
- No binding or validation between components

**Conclusion:**
- ✅ No compatibility issues
- ✅ Matches security-pcc official implementation
- ✅ Proper handling of first-boot creation and data recovery
- ✅ Safe to use

Delete VPhoneVirtualMachineRefactored.swift

refactor: integrate machineIdentifier into config.plist

Move machineIdentifier storage from standalone machineIdentifier.bin file
into the central config.plist manifest for simpler VM configuration.

**Changes:**
- VPhoneVirtualMachineManifest: Remove machineIDFile field
- VPhoneVirtualMachine: Load/create machineIdentifier from manifest
- VPhoneCLI: Remove --machine-id parameter, require --config
- Makefile: Remove --machine-id from boot/boot_dfu targets
- vm_manifest.py: Remove machineIDFile from manifest structure

**Behavior:**
- First boot: Creates machineIdentifier and saves to config.plist
- Subsequent boots: Loads machineIdentifier from config.plist
- Invalid/empty machineIdentifier: Auto-regenerates and updates manifest
- All VM configuration now centralized in single config.plist file

**File cleanup:**
- Move VPhoneVirtualMachineRefactored.swift to research/ as reference

Co-Authored-By: Claude Sonnet 4.6 <[email protected]>

docs/README_ko.md

@@ -94,13 +94,28 @@ make setup_machine            # "First Boot"까지의 전체 과정 자동화 (
 ```bash
 make setup_tools              # brew 의존성 설치, trustcache + libimobiledevice 빌드, Python venv 생성
 make build                    # vphone-cli 빌드 및 서명
-make vm_new                   # vm/ 디렉토리 생성 (ROM, 디스크, SEP 저장소)
+make vm_new                   # VM 디렉토리 및 매니페스트(config.plist) 생성
+# 옵션: CPU=8 MEMORY=8192 DISK_SIZE=64
 make fw_prepare               # IPSW 다운로드, 추출, 병합, manifest 생성
 make fw_patch                 # 부트 체인 패치 (일반 변형)
 # 또는: make fw_patch_dev     # 개발 변형 (+ TXM 권한/디버그 우회)
-# 또는: make fw_patch_jb      # 탈옥 변형 (+ 전체 보안 우회)
+# 또는: make fw_patch_jb      # 탈옥 변형 (dev + 전체 보안 우회)
 ```
 
+### VM 설정
+
+v1.0부터 VM 설정은 `vm/config.plist`에 저장됩니다. VM 생성 시 CPU, 메모리, 디스크 크기를 설정하세요:
+
+```bash
+# 사용자 정의 설정으로 VM 생성
+make vm_new CPU=16 MEMORY=16384 DISK_SIZE=128
+
+# 부팅 시 config.plist에서 설정 자동 로드
+make boot
+```
+
+매니페스트 파일은 모든 VM 설정(CPU, 메모리, 화면, ROM, 저장소)을 저장하며 [security-pcc의 VMBundle.Config 형식](https://github.com/apple/security-pcc)과 호환됩니다.
+
 ## 복원
 
 복원 프로세스를 위해 **두 개의 터미널**이 필요합니다. 터미널 2를 사용하는 동안 터미널 1을 계속 실행 상태로 두세요.