Fixes:
$ brew tap adamv/alt
...blah blah blah..
$ brew tap josegonzalez/php
...blah blah blah...
Warning: Could not tap josegonzalez/php/php over mxcl/master/php
Where it should be "over adamv/alt/php".
The symlinks taps write to Formula show up in git status, but this trick prevents this. brew-(un)tap maintain a .gitignore in Formula that contains all the symlinks brew-tap creates.
We add the .gitignore to the root .gitignore and TADA! Magic.