I don’t know if this changed after the Audacity changes to use autoconf, but when building Audacity on Ubuntu 13.10 using “make”, the Audacity binary is now placed in src/ rather than in the root of the source tree as always used to be the case.
So if you have not installed Audacity, you don’t have access to the shipped plug-ins as you did before.
Prior to the autoconf change, Audacity would pick up both the shipped plug-ins and built modules from within the source code tree. Now it doesn’t. (Debian).
Remind me, what was the benefit of the autoconf change?