Clean up private unused helpers in CLI and database reader code

[Widthdom]

Found while dogfooding the locally built cdidx on branch codex/search-audit-issues-20260619.

Duplicate check: no open issue found for private unused helpers QueryCommandRunner DbReader DbSymbolReader IndexLock cleanup stale dead code.

Evidence from cdidx unused --json --exclude-tests --visibility private:

• src/CodeIndex/Cli/IndexLock.cs:209 EscapeValue
• src/CodeIndex/Cli/QueryCommandRunner.cs:53 BatchJsonDocumentOptions
• src/CodeIndex/Cli/QueryCommandRunner.cs:10879 IsCSharpMetadataTargetOnlyReadinessDegraded
• src/CodeIndex/Database/DbReader.CSharpResolution.cs:902 TakeFirstCSharpBaseListEntry
• src/CodeIndex/Database/DbReader.References.cs:455 NormalizeRustMacroQuery
• src/CodeIndex/Database/DbReader.cs:166 ImpactAnchorReferenceKindsSql
• src/CodeIndex/Database/DbSymbolReader.cs:1755 HasExactDefinitionMatch

Problem:
These private helpers appear to have zero indexed references and are outside the previously filed dry-run/checkpoint cleanup issue.

Acceptance criteria:

• Confirm each candidate is truly unused, including partial-class and test-only call paths.
• Remove stale helpers or wire them intentionally.
• Add or update tests if behavior changes.