There are a few options depending on the layout of directories.
If all these repos are contained in a single root folder that you want to search, then you can search that directory explicitly by running
:CtrlP myproject. Alternatively, I believe you could say
let g:ctrlp_root_markers=['.root'] and make a .root file in the root (myproject) directory.
If for some strange reason you can't put all these directories in one root, you could make a directory somewhere else, put symlinks in it to all the directories you want searched, put
let g:ctrlp_follow_symlinks=1 in your .vimrc, and explicitly tell CtrlP to use this directory when running (
Failing that, you could modify
ctrlp_user_command, but doing so gets complicated and will ignore other ctrlp settings.