[Q] adding applications to custom rom questions

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Hi
in I have 3 questions about apps on custom roms

1: in some topics i read that people tried to put them in data/app or system/app . I guess system apps are not removable (or are partialy protected against uninstall). Or I am totaly wrong ... So what is the difference, where should i put the apps i wish to install ???


2: for some funny reason, some apps are installed, some not and some are visible but doesn't work .... What should i do to be sure that each app will work ??? should i first Zipalign or Deodex them ???

3: some apps require some configuration (for example i would like to add setcpu with profiling enabled to set the cpu at minimum when the display is off)
but how can i set this configuration in THE ROM so that i don't need to do it once the rom is installed ???

I don't remember off the top of my head, and I don't have access to my netbook with my data on it, but have you tried making a nandroid backup of your customized rom and pulling the ROM.zip file from within the backup and comparing your customized files between the backup rom.zip and the rom from your kitchen?

Edit; this was in reference to question three.