Cleanup source file dependency tracing logic

In cmTarget we trace the dependencies of source files in the target to
bring in all custom commands needed to generate them.  We clean up the
implementation to use simpler logic and better method names.  The new
approach is based on the observation that a source file is actually an
input (dependency) of the rule that it runs (compiler or custom) even in
the case that it is generated (another .rule file has the rule to
generate it).

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