cwl-runner validate fails after upgrade

The files are all existing and in correct folder structure after I moved them. Now when I run `cwl-runner --validate` I get this error below and `org.w3id.cwl.cwl.File` is no where in this yml file.

```
Tool definition file:///Users/****/****/UKBB/analysis-workflows/definitions_v1.1/tools/vep.cwl failed validation:
definitions_v1.1/tools/vep.cwl:5:1: checking field `requirements`
...more lines
...more lines
definitions_v1.1/types/vep_custom_annotation.yml:20:11: Field `type` references
unknown identifier `org.w3id.cwl.cwl.File`,
tried
file:///Users/brian/Bolton/UKBB/analysis-workflows/definitions_v1.1/types/vep_custom_annotation.yml#vep_custom_annotation/annotation/org.w3id.cwl.cwl.File,
```
The line is under `type: File` below
```
annotation:
type:
type: record
name: info
fields:
file:
type: File
label: 'File to be used for annotation, include index file'
```
However when I run cwl-runner validate on the vep.cwl tool itself it works

Reproduce the failure with `cwl-runner --validate` on `definitions_v1.1/tools/vep.cwl` and the referenced `definitions_v1.1/types/vep_custom_annotation.yml`. Start at the `requirements` and `annotation.file` entries shown in the report, then compare validation of the tool alone with validation through its references. Done means the upgrade result has a clear, reproducible validation outcome.

Written by the indexing model from the issue text.