Way to determine most popular Homebrew packages

Take the path that you used for --prefix= during your ./configure and sym-link that into the Cellar/ directory that Homebrew is using. Homebrew will see these directories and see the dependencies as satisfied (unless you need to have them compiled with or without certain features to make Homebrew's formulas compile correctly). If your manually-compiled deps aren't compiled correctly, you'll probably get errors out of Homebrew.

ln -s /path/from/prefix/ /usr/local/Cellar/path/from/prefix

(Note the trailing slash on the first path, and lack of trailing slash on the second. OS X can be picky about these slashes when creating sym-links.)

This is the wrong way to do it, you should just be using --ignore-dependencies coq — that's what it's there for.

brew update

Updates the Homebrew installation. If there are any errors, they should be reported by brew doctor. Try fixing them else, you could use the uninstall script as follows:

#!/bin/sh
# Just copy and paste the lines below (all at once, it won't work line by line!)
# MAKE SURE YOU ARE HAPPY WITH WHAT IT DOES FIRST! THERE IS NO WARRANTY!

function abort {
  echo "$1"
  exit 1
}

set -e

/usr/bin/which -s git || abort "brew install git first!"
test -d /usr/local/.git || abort "brew update first!"

cd `brew --prefix`
git checkout master
git ls-files -z | pbcopy
rm -rf Cellar
bin/brew prune
pbpaste | xargs -0 rm
rm -r Library/Homebrew Library/Aliases Library/Formula Library/Contributions
test -d Library/LinkedKegs && rm -r Library/LinkedKegs
rmdir -p bin Library share/man/man1 2> /dev/null
rm -rf .git
rm -rf ~/Library/Caches/Homebrew
rm -rf ~/Library/Logs/Homebrew
rm -rf /Library/Caches/Homebrew

And install homebrew again. Am pretty sure all this is configurable using puppet.