Default index-relationships to true

[matthewnitschke-wk]

--index-relationships was originally added, and relied on due to thinking an unrelated issue in uploaded files was due to it

This pr removes the concept of --index-relationships as a flag, and just defaults its concept to true

There is no good reason to disable relationship indexing, and doing so results in inconsistent scip generation files

[aviary3-wk]

Security Insights

No security relevant content was detected by automated scans.

Action Items

• Review PR for security impact; comment "security review required" if needed or unsure
• Verify aviary.yaml coverage of security relevant code

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Questions or Comments? Reach out on Slack: #support-infosec.

[matthewnitschke-wk]

QA +1

• CI does indeed pass

🚀 @Workiva/release-management-p 🚢

[rmconsole-wf]

+1 from RM