Fix some bugs in reading configs

[zerunz]

Description

This PR fixed some bugs in the logic of scip:

• Refactored SCIP configuration selection to consistently support monorepo-specific config with _default fallback, and - clarified the corresponding log messages.
• Fixed default index directory selection in createNewScipRegistry so _default SCIP directories are applied correctly when present.
• Fixed a watcher log formatting issue (%d → %q) for workspace root.
• Resolved a unit test panic caused by Go “typed nil” interfaces by adding a robust nil-check helper for registry.Registry and using it when creating registries.
• Addressed a potential nil dereference in hover() by avoiding writes to a nil *protocol.Hover result pointer.

Type of Change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Refactoring (no functional changes)
• Performance improvement
• Test improvement

Component(s) Affected

• Language Server (ULSP)
• SCIP Generation (Python utilities)
• VS Code/Cursor Extension
• Java Aggregator
• Build System (Bazel)
• Documentation
• Tests

Testing

• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes (bazel test //...)
• I have tested this manually with a real project

Manual Testing Details

Describe how you tested these changes:

• IDE used for testing:
• Project(s) tested against:
• Specific features/scenarios verified:

Checklist

• My code follows the existing code style and conventions
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• I have updated BUILD.bazel files if I added new source files
• My changes generate no new warnings
• Any dependent changes have been merged and published

Screenshots/Logs (if applicable)

Include any relevant screenshots, logs, or output that demonstrates the changes.

Related Issues

Fixes #(issue number)
Closes #(issue number)
Related to #(issue number)

Additional Notes

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