Except that the only familiar tool here seems to be the editor.[\QUOTE]
Not really. That is, the particular tools may be new, but the general process is something I'm quite familiar with, even if I more often cross-compile stuff for a BlueGene than a microprocessor
So if I look at your list, I get the following:
retain settings (Board, Serial Port, Library locations) - becomes a few shell script line, so I type say "set-ard" when I want to work on it.
Edit - Just like any other C code.
Pre-process - This is the unfamiliar one, but I'm guessing it's the process of turning a "sketch" into a real C program. If so, I'd much rather start with C.
Compile libraries and core code. - done once, creates say "arduino.a", which gets linked.
Compile sketch (using avr-gcc or avr-g++ as appropriate, and based on settings.)
Link with libraries and core. (avr-gld)
convert to uploadable format (avr-objcopy) - which condenses to a few lines in a Makefile, so I "just type make", or in my case hit the editor shortcut key, which conveniently lets me go to file:line of any errors, saving lots of time.
upload (using avrdude, according to settings.)
All of which is to say, rather long-windedly, that I've been programming for long enough to know what works well for me. Other people may work better with IDEs: that's why we have choices.
James