Q:

How to Debug MobileSubstrate Tweaks?

What is the best way to debug MobileSubstrate extensions, i.e. placing breakpoints etc.? Is there away to do this in Xcode? GNU Debugger?

A:

I use the syslog and tail. You'll need syslogd and Erica Utilities from Cydia. Then  throughout your tweak place NSLog(@"breakpoint 1 - %@", someObject); and run the tweak.
tail -f /var/log/syslog

A:

#define Debugger() { kill( getpid(), SIGINT ) ; }

Then you just call Debugger() wherever you want to place a breakpoint. 
You can also raise an exception if you want to trace the stack:
[NSException raise:@"Exception Message" format:formatString];

