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The Free Software Foundation, the organization behind the GNU project, has been unifying the build procedure for its tools for some time. Thanks to its tools `autoconf' and `automake', most packages now respond well to these simple steps, with no other intervention necessary:
./configure options make make install prefix=/usr/local/stow/package |
Hopefully, these tools can evolve to be aware of Stow-managed packages, such that providing an option to `configure' can allow `make' and `make install' steps to work correctly without needing to "fool" the build process.