Where does homebrew download software from

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.

This will be a synthesis of three things:

1. Making a homebrew formula that will dump the Applications you care about into the homebrew location. This will require some ruby knowledge and a short read of the homebrew wiki.
2. Making a script to copy/shove/move the files from the homebrew location to /Applications or ~/Applications or an alternate destination with administrator permissions
3. Learning enough about git to grab the tools. You likely won't be able to merge your "formula" with the homebrew repository since it's against their policy to re-distribute software you don't possess the permission (rights) for software code publication.

If you want to do this as a learning exercise, have a great time learning. There are far better tools to package OS X binaries like Package Maker, JAMF's Composer, or Iceberg.

If you were uncertain if homebrew was your best option, I'd start with Iceberg and a tutorial like this to handle the permissions.