I actually went through the setup.rb and was surprised they don't do it. Rails itself will raise the exception if the initializer does not exist IIRC, so just removing the file and .gitignoring it would do.
There is talk about more general solutions here:
https://groups.google.com/d/msg/rubyonrails-core/N2EFnf6X_i4...
Btw: you can check the regenerated file into the repo, adding it to .gitignore just prevents you from accidentally adding it:
Last login: Tue Jan 15 17:07:14 on ttys005
Voice-of-Evening:~ fgilcher$ cd /tmp
Voice-of-Evening:tmp fgilcher$ git init test
Initialized empty Git repository in /private/tmp/test/.git/
Voice-of-Evening:tmp fgilcher$ cd test/
Voice-of-Evening:test fgilcher$ echo "README" >> .gitignore
Voice-of-Evening:test fgilcher$ touch README
Voice-of-Evening:test fgilcher$ git status
# On branch master
#
# Initial commit
#
# Untracked files:
# (use "git add <file>..." to include in what will be committed)
#
# .gitignore
nothing added to commit but untracked files present (use "git add" to track)
Voice-of-Evening:test fgilcher$ git add -f README
Voice-of-Evening:test fgilcher$ git status
# On branch master
#
# Initial commit
#
# Changes to be committed:
# (use "git rm --cached <file>..." to unstage)
#
# new file: README
#
# Untracked files:
# (use "git add <file>..." to include in what will be committed)
#
# .gitignore
Voice-of-Evening:test fgilcher$