I am not quite comfortable at the fact that a user would have to change the workflow from using input to depends, or vise versa if he or she would like to turn on/off tracing dependencies of existing dependencies. It would make sense to introduce an option to

1. If the option is turned on, SoS will try to trace the dependencies of all existing targets, including the ones in input and in depends statements.
2. If the option is turned off, SoS operates in the usual Makefile style, namely not tracing dependencies.

The option could be named -D (dependency) or -T (tracing), although it is a bit difficult to explain this concept very quickly to users.

Note that the existing behavior is more flexible in that it allows part of the workflow to be dependency tracing and part of it non-dependency tracing.