Design problem: etc that is not /etc? other pseudo subdirectories and instance handling?

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Hello, For various reasons such as accomodating a package that can
have multiple instances on a server I have an etc subdirectory that is
not intended for /etc holding configuration files that I want to
ultimately reside in /opt/mypackage/instance/etc What is the best way
to handle this situation? I've been able to get this to work in a
kludgy rpm way in the past with this and other files that best reside
in their own subdirectory group like /opt/mypackage/instance/bin,
/opt/mypackage/instance/doc but currently they are not nicely laid out
like that in my rpmbuildroot . I currently have it in
rpm_build_root/SOURCES/etc but I suspect that this will ultimately put
the files into /etc by default and want to avoid this again for
various reasons such as having multiple instances. A caveat is that
this package is particularly large: 160Mb with a large 120Mb database
file. Any suggestions or the best way of handling all this are
appreciated.

Specific Questions:

1) Best way to do packages that can create multiple instances of themselves?
2) Best way to handle subdirectories that you would like to name etc,
bin... but that will not ultimately reside in /etc, /bin (see 1)?
3) Easily deletable instances such as with rm -Rf /opt/mypackage/instance?

In writing this I wonder if I am simply going to have to have
post-install bash commands to install and delete instances. I was
hoping to avoid that.

-- IV
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