Description
This PR fixes a couple of bugs in the .dockstore.yml inference code:

• During the inference process, workflow files that are referenced from other workflow files should be eliminated from consideration as primary descriptors. This was broken, causing every workflow file (files named with the appropriate suffix, for example wdl) to be considered as the primary descriptor of an entry, creating potentially many spurious entries for helper files in the resulting .dockstore.yml. The root cause was an errant path manipulation that was probably introduced during the Path conversion. Fixed.
• Fixes debug output which records the size of the github ref's Zip.

It also resets to the SNAPSHOT version.

Originally, this PR included a tweak that constructed a GitHub ref where a branch name was being used, avoiding some default output and maybe some extra requests. However, the unfixed code seems to [eventually?] do the right thing, and to avoid unintended consequences this late in the deploy cycle, I removed the change.

Review Instructions
Infer a .dockstore.yml for github.com/PacificBiosciences/HiFi-human-WGS-WDL and confirm that the inferred .dockstore.yml contains two entries.

Issue
https://ucsc-cgl.atlassian.net/browse/SEAB-6531

Security and Privacy

If there are any concerns that require extra attention from the security team, highlight them here and check the box when complete.

• Security and Privacy assessed

e.g. Does this change...

• Any user data we collect, or data location?
• Access control, authentication or authorization?
• Encryption features?

Please make sure that you've checked the following before submitting your pull request. Thanks!

• Check that you pass the basic style checks and unit tests by running mvn clean install
• Ensure that the PR targets the correct branch. Check the milestone or fix version of the ticket.
• Follow the existing JPA patterns for queries, using named parameters, to avoid SQL injection
• If you are changing dependencies, check the Snyk status check or the dashboard to ensure you are not introducing new high/critical vulnerabilities
• Assume that inputs to the API can be malicious, and sanitize and/or check for Denial of Service type values, e.g., massive sizes
• Do not serve user-uploaded binary images through the Dockstore API
• Ensure that endpoints that only allow privileged access enforce that with the @RolesAllowed annotation
• Do not create cookies, although this may change in the future
• If this PR is for a user-facing feature, create and link a documentation ticket for this feature (usually in the same milestone as the linked issue). Style points if you create a documentation PR directly and link that instead.