Ninja: Consider only custom commands deps as side-effects (#14972)

Since commit v2.8.12~248^2 (Ninja: Custom Command file depends don't
need to exist before building, 2013-06-07) all explicit dependencies
inside build folder were considered as possible build command
side-effects and phony rules were produced for them in case they don't
exist when starting to build. This is unnecessary since regular compile
inputs need to exist or cmake will fail.  Moreover the exception for
sources having GENERATED property that can be missing is already handled
by WriteAssumedSourceDependencies.

This fixes unwanted phony rules for all regular source files when doing
in-source build, causing Ninja not complain when such files gets missing,
i.e. during development. Also this reduces number of rules in ninja.build.

Now only custom command dependencies are considered as possible side-effects.

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