Secondary files can be picked up from nested tools independent of workflow

## Expected Behavior
I would expect that I should be able to look at a workflow and see all the input files that it requires.
i.e. cwltool should warn/reject workflows that define additional inputs buried in tools as opposed to the "root" workflow

## Actual Behavior
It seems that secondary files can be defined at the tool level and cwltool picks them up "properly" meaning that someone using a workflow will need to review both the workflow and all imported tools in order to get a complete picture as to what input is required.

(Unfortunately, addressing this seems to be a breaking change. Note that the ticket this was originally raised in was https://github.com/common-workflow-language/common-workflow-language/issues/362 )

## Workflow Code
https://gist.github.com/denis-yuen/730b3504732bcb26f65bd2e4544ca8b0
(content of input bam files and index files is irrelevant)

## Resulting behaviour
```
cwltool workflow.redundant.cwl workflow.test.json
cwltool workflow.cwl workflow.test.json
```
both lead to "success"

## Your Environment
* cwltool version: 1.0.20180116213856