I'm more interested to know the answers to these questions:
 - How does one deploy an application on Pharo that requires a one-line change to a core system method that is not acceptable to the Pharo gods?
The same tha squeak for changes that aren't accepted/belongs to/are too specific to an application. You include them as an *mypackage extension in some package of yours and then when the mcz is installed, the extension is installed too. That is just monticello as always.
I'm talking about an override not an extension.
 - How does one deploy an application on Pharo that loads code from external web-sites?
Using doIts if necessary.
Right, dropping down into straight load-script and doing it. Got it! :)
 - How does one deploy an application on Pharo that requires external graphics, videos, XML or other resources?
Idem.
Often specific _versions_ of resources go with each specific version of an application. Now I am maintaining those separately, in separate places using separate tools. I want something to expand the metaphor of an object being "encapsulated behavior + state" into my deployment system, so it will be "encapsulated behaviors + resources". Thankfully, even Pharo 1.3 still supports .SAR files, but no nice GUI to load them, just the file-manager. :(
 - How does one deploy an application on Pharo that requires an object-graph to be loaded internally into the image that was pre-built using another tool (e.g., NOT generated via code)?
Don't understand the example
A better example. What if I just want something that strips my image down of lots of code and objects, without leaving any new code loaded? It's a rhetorical question, I already know the answer: Create a Metacello config to host only a load-script (doIt). But I wonder whether said doIt would be able to "unload itself" when it was done? Probably could.
I think it does those things, maybe a second look at the existings configurations can clear a lot of doubts.
The picture seems to be, as long as my app is all just "clean-loading MC packages", then I can use Metacello within its normal bounds. (OR, I could just use the standard "lighter-weight" SCM tools; Monticello + MonticelloConfigurations + Gofer). However, if an application requires anything additional: overrides, resources or special-configurations, then I drop down to the "ultimate flexbility" afforded by doIt's - which is just load-scripting. Even then, the resources are not encapsulated as I already said. SqueakMap is a repository that hosts load-scripts encasulated with or without resources. It's perfectly complimentary to all of the other tools. I'm exhausted of talking about this.. Regards, Chris