Revert commit 7243c951 (Ninja: Don't limit custom cmd side-effects to
build folder, 2014-06-27) because it causes every custom command
dependency in the source tree to get a phony rule.  For large projects
these rules get too big for Ninja to handle efficiently.  While the
original change addressed a valid concern, it did not seem to occur
regularly in practice because well-behaved projects generate their
side-effects only in the build tree.  Until we support explicit
specification of side-effects (CMake issue #14963), we will have to use
this as a middle-ground.