[Windows Mobile] kokotas:
v1.2.1.0

An updated version is up @ 1st post.

I think this bug is fixed now.

I downloaded that rom and tested it and all the packages are sorted correctly as far as I can see!

I changed a little how the application handles comments:

If /k is given the application will keep all the original comments.

If /k is omitted the application will keep only some basic comments. For example:

initflashfiles.dat

root:-Directory("My Documents")
root:-Directory("Program Files")
Directory("My Documents"):-Directory("我的图片")
Directory("\My Documents\我的图片"):-File("春天.jpg","\Windows\Spring.jpg")
Directory("\My Documents\我的图片"):-File("青草.jpg","\Windows\Grass.jpg")
Directory("\My Documents\我的图片"):-File("绿叶.jpg","\Windows\Leaf.jpg")
Directory("\My Documents\我的图片"):-File("水纹.jpg","\Windows\Water.jpg")
Directory("My Documents"):-PermDir("模板")
Directory("Program Files"):-Directory("连接")
Directory("\Windows"):-Directory("Help")
Directory("\Windows"):-Directory("Fonts")
Directory("\Windows"):-Directory("程序")
Directory("\Windows"):-Directory("StartUp")
Directory("\Windows"):-PermDir("“开始”菜单")
Directory("\Windows"):-Directory("Temporary Internet Files")
Directory("\Windows"):-Directory("AppButtons")
Directory("\Windows"):-Directory("收藏夹")
Directory("\Windows"):-Directory("Rings")
Directory("\Windows"):-Directory("AppMgr")
Directory("\Windows"):-PermDir("System")
Directory("\Windows\System"):-PermDir("ConfigMgr")
Directory("\Windows\System"):-PermDir("CertDtls")
Directory("\Windows\System"):-PermDir("DumpFiles")
Directory("\Windows\System"):-PermDir("CabQueue")
; Start Menu contents
Directory("\Windows\“开始”菜单"):-PermDir("程序")
Directory("\Windows\“开始”菜单"):-PermDir("设置")
Directory("\Windows\“开始”菜单\程序"):-File("帮助.lnk","\Windows\help.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("搜索手机.lnk","\Windows\search.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("电话.lnk","\Windows\cprog.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("任务.lnk","\Windows\tasks.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("调制解调器链接.lnk","\Windows\ATCIUI.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("Internet 共享.lnk","\Windows\IntShrUI.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("任务管理器.lnk","\Windows\TaskMgr.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("ActiveSync.lnk","\Windows\sync.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("日历.lnk","\Windows\calendar.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("联系人.lnk","\Windows\addrbook.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("Internet Explorer.lnk","\Windows\pie.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("PerfMan.lnk","\Windows\perfman.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("电子邮件.lnk","\Windows\tmailpicker.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("短信.lnk","\Windows\tmailsms.lnk")
Directory("\Windows"):-File("设置电子邮件.lnk","\Windows\acctwiz.lnk")
; turn off the OLD inbox later
; put the OLD inbox to the program floder (temporary)
Directory("\Windows\“开始”菜单\程序"):-File("便笺.lnk","\Windows\notetake.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("图片和视频.lnk","\Windows\pimg.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("SimTkUI.lnk","\Windows\SimTkUI.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("计算器.lnk","\Windows\calc.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("资源管理器.lnk","\Windows\fexplore.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("入门.lnk","\Windows\WelcomeCenter.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("闹钟.lnk","\Windows\MSAlarms.lnk")
Directory("\Windows\“开始”菜单\程序"):-Directory("游戏")
Directory("\Windows\“开始”菜单\程序\游戏"):-File("纸牌.lnk","\Windows\solitare.lnk")
Directory("\Windows\“开始”菜单\程序\游戏"):-File("icon.lnk","\Windows\gamesico.lnk")
; App Button default links
Directory("\Windows\AppButtons"):-File("日历.lnk","\Windows\calendar.lnk")
Directory("\Windows\AppButtons"):-File("联系人.lnk","\Windows\addrbook.lnk")
Directory("\Windows\AppButtons"):-File("任务.lnk","\Windows\tasks.lnk")
Directory("\Windows\AppButtons"):-File("录音.lnk","\Windows\voice.lnk")
Directory("\Windows\StartUp"):-File("bugtrap.lnk","\Windows\bugtrap.lnk");
Directory("\Windows\StartUp"):-File("poutlook.lnk","\Windows\poutlook.lnk")
Directory("\Windows\StartUp"):-File("欢迎使用.lnk","\Windows\welcome.lnk")
Directory("\Windows\“开始”菜单\程序"):-File("远程桌面 Mobile.lnk", "\Windows\wpctsc.lnk")
Directory("Program Files"):-Directory("Windows Media Player")
Directory("\Windows\“开始”菜单\程序"):-File("Windows Media.lnk","\Windows\WMPlayer.lnk")
Directory("\Program Files\Windows Media Player"):-File("默认(纵向).skn","\Windows\wmp_WPC_portrait.lnk")
Directory("\Program Files\Windows Media Player"):-File("默认(横向).skn","\Windows\wmp_WPC_landscape.lnk")
Directory("\Program Files\Windows Media Player"):-File("默认(方格).skn","\Windows\wmp_WPC_square.lnk")
Directory("\Program Files\Windows Media Player"):-File("欢迎使用 Windows Media.wma","\Windows\wm_start.lnk")
; Help .LNK files
Directory("\Windows\Help"):-File("ActiveSync.lnk","\Windows\h_sync.lnk")
; Transcriber available for USA, FRA & GER
Directory("\My Documents\模板"):-File("空白文档.pwi","\Windows\blank.pwi")
Directory("\My Documents\模板"):-File("会议记录.pwi","\Windows\meeting.pwi")
Directory("\My Documents\模板"):-File("备忘录.pwi","\Windows\memo.pwi")
Directory("\My Documents\模板"):-File("电话备忘录.pwi","\Windows\phone.pwi")
Directory("\My Documents\模板"):-File("示例文档.pwi","\Windows\sample.pwi")
Directory("\My Documents\模板"):-File("待办事宜.pwi","\Windows\todo.pwi")
Directory("My Documents"):-Directory("个人")
Directory("My Documents"):-Directory("商务")
Directory("My Documents"):-Directory("我的音乐")
Directory("My Documents"):-Directory("我的铃声")
Directory("\Windows"):-File("cmclient.exe","\Windows\HTC_cmclient.exe")

app.dat

;ALBUM
Directory("\Windows\“开始”菜单\程序"):-File("相册.lnk","\Windows\Album.lnk")
Directory("\Windows\Help"):-File("相册.lnk","\Windows\Help_Album.lnk")
Directory("\My Documents\我的图片"):-File("Albums Sample_01.jpg","\Windows\Albums Sample_01.jpg")
Directory("\My Documents\我的图片"):-File("Albums Sample_02.jpg","\Windows\Albums Sample_02.jpg")
Directory("\My Documents\我的图片"):-File("Albums Sample_03.jpg","\Windows\Albums Sample_03.jpg")
Directory("\My Documents\我的图片"):-File("Albums Sample_04.jpg","\Windows\Albums Sample_04.jpg")
Directory("\My Documents\我的图片"):-File("Albums Sample_05.jpg","\Windows\Albums Sample_05.jpg")
Directory("\My Documents\我的图片"):-File("Albums Sample_06.jpg","\Windows\Albums Sample_06.jpg")
Directory("\My Documents\我的图片"):-File("Albums Sample_07.jpg","\Windows\Albums Sample_07.jpg")

EDIT:

I added more stability to the application:

When I run it on an old rom's dump (the ones that weren't organized into "PACKAGES_*") the application would crash!

With v1.2.1.0 it should work ok!

I've tested it with some Elfin official roms and it's NOT crashing:)

Regards!