The changes to the new build system from IOhannes leaves the .pd_linux files in individual ".libs" subdirs. They should be in the correct place to be useable without an install, like the old build system.
Anonymous
if we want the new system to behave exactly like the old system, then i wonder why we want to change the system :-)
anyhow.
attached is a patch that creates symlinks from the default output (which is e.g. extra/stdout/.libs/stdout.pd_linux) to the one you are used to (extra/stdout/stdout.pd_linux) when building, and removes them when cleaning.
please test it, especially on systems that don't have symbolic links.
git patch (apply with "git am <file>") against todays git</file>