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cygport: How to use to build and install modified packages

In my experimentation with run (see preceding post with subject
"run-1.3.3-1: Unicode text and empty args") I somehow managed to build a
modifed version of a released package (run-1.3.3-1) but feel I have not
found the right way of performing this task - so I ask for some advice (or
referral to some How-To?) based on how I did it:
- Get source: I did that via setup which placed the cygport-file
(run.cygport) and source-archive in /usr/src
- Unpack source: I wanted to do "cygport run prep" - but that failed to
recognize the cygwin-run-1.3.3.tar.bz2 archive and I had to do "cygport run
download" which downloaded cygwin-run-run.tar.bz2 instead. Why?
- Compile: I did "cygport run compile" to get started, then modified sources
and re-compiled (to sidestep the time-consuming configuration step) in
build/src with "make".
- Install: I thought I could install with "cygport run install" - but that
installed in the staging area within the pacakge source-tree only. So I
installed with "make install" for the time being. What is the right way,
maybe using setup after packaging the modified package?
- Package: "cygport run package" works as expect, including creating patches
- but the resulting packages (in dist) were run-run-run.tar.xz and
run-src.tar.xz - so the version is somehow getting trashed within cygport.
Does the cygport file at the outset need to be renamed to include the
Regards, Martin

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