I am working on the AIME codebase, in C++, and have a problem where seasonal descriptions for rooms doesn't appear to be working correctly. Now, assuming I am setting the flags correctly, which is a big assumption, I went on to look at the code and made a change I hoped would help. I then did a make clean, followed by a ./configure and a new make install. I noticed however that it did not prompt me for new file folders as it did on my first install. Does the new make use the altered code or does that code come from somwhere else, or does anyone have a clue? I guess what I am asking is, custumarily, if you make a change to source code is that the way to go about getting the code into the executeable/mudbin/whatever you call in linux/C++ applications?

This seem a bit overkill. Just 'make' by itself should do what you need done. The above is important if you change the makefile. 'make clean' removes compiled object files, and './configure' rebuilds a new makefile if the system configuration has been changed. 'make install' apparantly creates some new subdirectories as well as compiling the source files.

No, because they were already there.

Yes, the new make use the altered source files to generate code.
As I wrote above, it's a bit of overkill. THe 'make' program is smart enough to chekc file access dates, so it can decide which object files need to be updated before linking. Unless you've changed your system setup (kernel, compiler, libraries), there's no reason to either make clean<*> or run configure;
Just cd to your src/ dir and type 'make' when you've made a change.

<*> sometimes running 'make clean;make' can fix some linking issues, but generally it's not needed unless you're making a backup of your code and don't want all those bulky .o files in your tar file.