Project based searching within Emacs can be done using projectile.
It allows for per-project configuration of ignore files (in a <projectroot>\.projectile file), or specify subdirectories to monitor and ignore all others.
It can run grep, ack (requires ack-and-a-half.el) and ag (ag.el) on files within the defined project (either based on the .projectile file or by finding a supported VC file to define a project root).