Isn't all the configuration done via ./tools/make_makefiles ?
No, not all.
I thought that if you want to add anything to wine you:
1 - simply add it to git 2 - ./tools/make_makefiles 3 - autoconf 4 - ./configure 5 - make depend && make
Is this wrong?
Yes. On occasion we need to add or improve checks for different libraries. tools/make_makefiles is used to add new code to Wine, configure.ac is modified to add new configure checks.
The use of configure.ac is well-described on the GNU autoconf page. --Juan