Hi,
for info:
For those who doesn't want pd auto-connect to jack (for use with qjackctl patchbay or ladish), there is the "no-self-connect" patch from Nedko Arnaudov (for jack2). Check if the package from your distro compile jack with it, or you'll have to compile yourself (git branch or download it):
http://nedko.arnaudov.name/blog/2012/12/19/jack-1.9.9.5-no-self-connect-patch.html

related feature request:
http://sourceforge.net/tracker/?func=detail&aid=3519504&group_id=55736&atid=478070

KXstudio (or just kxstudio repositories), implement it in the great jack manager Cadence: you can choose to prevent apps self connecting to system ports, or to any ports.

you can then use pd with ladish, (add an app with command "pd-extended", followed by the path and file name you need to open). All your connections will be saved and no need to disconnect all first.

enjoy it
r