debugAtAllCosts has not been ported to 0.9 yet. It is unclear yet if it will be. I would prefer to have a version of it ported, but it is unclear if that is the project direction. I think folks are hoping that the tools will provide the functionality. For Firebug, you could try the Fireclipse version of the Firebug plugin that allows you to see and debug JS code that is evaled.

Fireclipse:
http://www.almaden.ibm.com/u/bartonjj/fireclipse/index.html

I'm just starting to use 0.9, and haven't figured out how to debug the old-fashioned way yet. The normal dojo.debug() doesn't seem to work. You can use console.debug() , which will write to firebug if you have it, or will create a debug console at the bottom of your browser if not.

This helps debuging really a lot, since breakpoints can be set on all the loaded js files.
Currently it seems not so convenient to take a deep debuging on dojo0.9

I'm porting an app from 0.4 to 0.9 and writeIncludes is the feature that I'm missing most :-(

As far as setting breakpoints, you can try the Fireclipse Firefox extension, which extends Firebug with support for debugging/setting breakpoints in evaled code. But it is not necessarily a complete solution if you want to do deep debugging in other browsers (one version of the Microsoft debugger has support for seeing evaled code, but I forget which one, maybe the Microsoft Script Editor?). You can also try just doing a script tag that loads the JS file directly, but it can be tricky to work out the right load order to put the tags in the right order.

Feel free to voice your concern/cast your vote for something more like the traditional debugAtAllCosts here:
http://trac.dojotoolkit.org/ticket/3583
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