Hello!
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1. What to Put In The Removal/Instalation scriprts
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there is no secret, install all what your program depends to work: binaries, config files, static/shared libs, directories, etc.
and for removal, remove all that is relative to your program. Do not remove anything that may be being used for another programs.
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2 What executable number to give them and how (chmod 700 ./prerm.sh was my closest guess)
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in fact you should ask yourself:
who can use my program?
it can damage the system?
who should have permission to remove the binaries?
who should be permitted to modify the config files?
based on the answers you can set the permissions well.
if you don't know answer some of this questions,or if you want some tip, look on your system for an similar program and see what permissions it have set.
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How to Make a Directory in ~/
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the ~/ directory is just where the environment variable $HOME points to.