Is it possible to trace what exactly Magento is doing?

Is it possible to see the route chosen, controll开发者_开发百科er, etc.?

I know I can turn on the inline tracing but that doesn't really seem sufficient.

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Look into Alan Storms Commerce Bug module and I would highly recommend setting up X-Debug.

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Tracing what Magento is doing and how the code flow works

Best way is to use PHP IDE like Eclipse along with Debugger like Xdebug.

Here are some useful links on Debugging PHP applications with Xdebug:-

http://www.eclipse.org/pdt/articles/debugger/os-php-eclipse-pdt-debug-pdf.pdf

http://devzone.zend.com/article/2930