I maintain my own software stack in /usr/local - applications that don't come with the operating system, or different version of ones that do.
I was just updating gzip. So the ./configure script, when invoked with --help, says:
By default, `make install' will install all the files in
`/usr/local/bin', `/usr/local/lib' etc. You can specify
an installation prefix other than `/usr/local' using `--prefix',
for instance `--prefix=$HOME'.
OK, so I do ./configure, make, make install.
What the heck?!?!?!
It's installed it in /usr, overwriting the system copies!
Looking at the configure output in more detail, it did say:
checking for prefix by checking for gzip... /usr/bin/gzip
I know I can't blame autoconf itself for this one, because the tool has been misused, but using a tool and then violating both its common conventions (default prefix of /usr/local) and its own self-documenting behaviour, is really bad.
And one last thing. It installs itself as zcat, not gzcat. On Solaris, zcat isn't even the same beast.