Yesterday I learned that Pd 0.48 app bundle for OSX no longer has the src dir embedded. It was brought to my attention by Alexandre Torres Porres and explained by Dan Wilcox in the context of the issue that pdlibbuilder now has when trying to find the API (https://github.com/pure-data/pd-lib-builder/issues/33#issuecomment-322384696). Though it only takes a few keystrokes to modify pdlibbuilder's search path for the includes, I'd like to be sure that omitting the src dir from the bundle is what everyone wants.
What I recall and understand from Miller's explanation during PdCon16~ about his Pd distributions is, for each platform he makes a source distribution with platform-specific goodies included. Then he builds, and in resulting distributions both source and binaries are included so that everyone can easily reproduce the build. The workflow was explained during a 'round workbench' session and later summarized in a presentation, see https://github.com/pure-data/pd-lib-builder/issues/33#issuecomment-322384696 (9:10 and 10:00).
Dan was unaware of this when reorganizing the build scripts for the bundle, and while I'm writing this he opened an issue suggesting a fix: https://github.com/pure-data/pure-data/issues/181
Katja