Fix DB URI display and stable output paths

[Widthdom]

Summary

• Preserve SQLite file: URI display values for cdidx db and cdidx diff reports.
• Normalize report --db file:... before schema collection and stabilize report bundle output paths.
• Stabilize export archive / ctags output paths and treat import WAL/SHM cleanup as best-effort after DB replacement.
• Keep DB path metadata probes best-effort for expected filesystem and path exceptions.

Validation

• dotnet build
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~DbCommandRunnerTests"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~DiffCommandRunnerTests"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~ReportCommandRunnerTests"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~ExportImportCommandRunnerTests"
• dotnet test tests/CodeIndex.Tests/CodeIndex.Tests.csproj --filter "FullyQualifiedName~DbPathResolverTests"
• dotnet test
• dotnet run --project tools/CodeIndex.Changelog -- check
• dotnet format CodeIndex.sln --verify-no-changes
• git diff --check origin/main..HEAD
• dotnet ./src/CodeIndex/bin/Debug/net8.0/cdidx.dll status --check --json
• Adversarial review of origin/main..HEAD: No blocking/actionable issues found.

Changelog

• changelog.d/unreleased/3221.fixed.md
• changelog.d/unreleased/3148.fixed.md
• changelog.d/unreleased/3147.fixed.md
• changelog.d/unreleased/3138.fixed.md
• changelog.d/unreleased/3125.fixed.md
• changelog.d/unreleased/3175.fixed.md

Follow-up Candidates

None.

Fixes #3221
Fixes #3148
Fixes #3147
Fixes #3138
Fixes #3175
Fixes #3125