28 files? There goes my guess about compiling just one file. I should have thought twice about it.
At this point you are going further than I have ever been. I was used to, say, manually patch realtime extensions into a kernel version that wasn't the intended one (when realtime patches were still not merged into mainstream kernel). So automatically patching the source would fail, but one could find the right places to patch manually by just looking at the code. There was usually a whole bunch of files to patch, but it was quite an easy task that called for very little programming knowledge.
I'm into system administration, not programming. However, you are about to code/debug, etc, by yourself. You'll need to learn more about programming than I currently know. So take what I'm going to write with a grain of salt. Others in this forum will know about programming much better than me, perhaps they could help from this point forward.
I guess it could be done in eclipse and gdb, yes. But to learn about how the builds work, I would:a) learn about autotools, then b) look at the source code.
I think that would be the fastest way to learn. I have never, ever, used an IDE for any build. Software was built that way, much before anyone could heard anything about Eclipse. And Eclipse (I guess) will use the autotools infrastructure anyway.
Usually just getting in the upper directory of the source and using the configure/make/make install litany, would be enough. Makefiles do the magic. They will have the calls to gcc, with the different options, etc, so you don't need to call gcc manually for each file.
Then I'm pretty sure that, by looking at source code and Makefiles, you'll find many, many clues. You'll have to dwell there for some time, I'm afraid, but again, quite probably that will be the fastest way to get the needed skills. The knowledge so achieved will be useful no matter which distro you are using, right now or in the future, debian-based, redhat-based, slackware, whatever.
After that, I think you could easily go with that knowledge to Eclipse and have a successful, quite fast transition to work with that IDE, should you still think you need it.
You are going to embark yourself into a quite interesting experience. I wish you good luck and lots of fun.